1.1A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning.Meng LIUICEO: Ontology of Integrative and Conjugative ElementsThe ICEO Ontology is licensed under CC BY 4.0.02-27-2019Meng LIUA biological ontology in the domain of Integrative and Conjugative Elements.This is an ICE ontology 1.0Yongqun Hehttp://creativecommons.org/licenses/by/4.0/Hong-Yu OuRelates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.Really of interest to developers onlyBFO OWL specification labelBFO OWL specification labelRelates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2Person:Alan RuttenbergReally of interest to developers onlyBFO CLIF specification labelBFO CLIF specification labeleditor preferred labeleditor preferred labeleditor preferred termeditor preferred termeditor preferred term~editor preferred labelThe concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)PERSON:Daniel SchoberGROUP:OBI:<http://purl.obolibrary.org/obo/obi>editor preferred labeleditor preferred labeleditor preferred termeditor preferred termeditor preferred term~editor preferred labelexampleA phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are notPERSON:Daniel SchoberGROUP:OBI:<http://purl.obolibrary.org/obo/obi>example of usageexample of usagehas curation statusPERSON:Alan RuttenbergPERSON:Bill BugPERSON:Melanie CourtotOBI_0000281has curation statushas curation statusdefinitiondefinitiondefinitiontextual definitiontextual definitionThe official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.2012-04-05:
Barry Smith
The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.
Can you fix to something like:
A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.
Alan Ruttenberg
Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria.
On the specifics of the proposed definition:
We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition.
Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable.
We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel SchoberGROUP:OBI:<http://purl.obolibrary.org/obo/obi>definitiondefinitiondefinitiontextual definitiontextual definitioneditor noteAn administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.PERSON:Daniel SchoberGROUP:OBI:<http://purl.obfoundry.org/obo/obi>editor noteeditor noteterm editorName of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.PERSON:Daniel SchoberGROUP:OBI:<http://purl.obolibrary.org/obo/obi>term editorterm editorMiaalternative termalternative termdefinition sourceformal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007PERSON:Daniel SchoberDiscussion on obo-discuss mailing-list, see http://bit.ly/hgm99wGROUP:OBI:<http://purl.obolibrary.org/obo/obi>definition sourcedefinition sourcecurator notecurator noteimported fromimported fromexpand expression toexpand expression toOBO foundry unique labelOBO foundry unique labelelucidationelucidationhas associated axiom(nl)has associated axiom(nl)has associated axiom(fol)has associated axiom(fol)An annotation property that represents the ID of oriT sequence in the oriT database oriTDB.Meng LIU (Mia), Oliver Hehas oriTDB accessionAn annotation property that represents the ID of a ICE/IME/CIME in the ICE database ICEberg.Meng LIU (Mia), Oliver Hehas ICEberg accessionAn annotation property that represents the ID of a T4SS sequence in the T4SS database SecReT4.Meng LIU (Mia), Oliver Hehas SecReT4 accessionhas SecReT4 accessionAn annotation property that represents the hyperlink of a oriT sequence in the oriT database oriTDB.Meng LIU (Mia), Oliver Hehas oriTDB hyperlinkAn annotation property that represents the hyperlink of a ICE/IME/CIME in the ICE database ICEberg.Meng LIU (Mia), Oliver Hehas ICEberg hyperlinkhas ICEberg hyperlinkReannotated signature proteins by ICEberg.protein reannotated roleprotein reannotated roleGI number is a series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record.Meng LIU (Mia), Oliver Hehas NCBI GI numberhas NCBI GI numberAn annotation property that represents the length of a sequence or how big something isMeng LIU (Mia), Oliver Hehas_sizehas_sizeAn annotation property that represents which species that a ICE or a moblie genetic element can transfer to.Meng LIU (Mia), Oliver Hespecies can be transferred toan annotation property that represents the completeness of the sequence.Meng LIU (Mia), Oliver Hesequence statussequence statusAn annotation property that represents the ID of a ICE sequence or the host genome in the NCBI GeneBank database.Meng LIU (Mia), Oliver Hehas NCBI GeneBank accessionhas NCBI GeneBank accessionGC-content (or guanine-cytosine content) is the percentage of nitrogenous bases on a DNA or RNA molecule that are either guanine or cytosine (from a possibility of four different ones, also including adenine and thymine in DNA and adenine and uracil in RNA).Meng LIU (Mia), Oliver Hethe number outside the square brackets are the GC content of the ICE while the number inside the square brackets are the GC content of the host genomeGC content[Genome]GC content[Genome]the coordinates of genetic elements or genes in the chromosomeMeng LIU (Mia), Oliver Hegenome coordinatesgenome coordinatesconfirmation status inculdes: experimental verified; predicted in silico; not sureMeng LIU (Mia), Oliver Heconfirmation statusAn annotation property that represents a ICE or a mobile genetic element has transfer interaction with IME.Meng LIU (Mia), Oliver Hehas interaction with IMEMeng LIU (Mia), Oliver HeAn annotation property that represents a ICE or a mobile genetic element has transfer interaction with CIME.has interaction with CIMEAn annotation property that represents theMeng LIU (Mia), Oliver Heinsertion siteinsertion siteA GeneID in the NCBI Gene databaseOliver He, Yue LiuNCBI GeneIDNCBI GeneIDthe NCBI LocusTag name of a geneOliver He, Yue LiuNCBI LocusTagNCBI LocusTaga date of content modificationOliver He, Yue Liumodification datemodification dateThe NCBITaxon ontology ID of an organism.Oliver He, Yue Liuorganism NCBITaxon IDorganism NCBITaxon IDA chromosome ID where a gene is located.Oliver Hechromosome ID of genechromosome ID of genean annotation property that specifies the type of a geneOliver Hetype of genetype of genean annotation property that specifies a nomenclature statusOliver Henomenclature statusnomenclature statusAn annotation property that represents a gene's association with PubMed publication(s).Yongqun HeYH: use the format:
PMID: pmid1, pmid2, ...
where pmid1 and pmid2 are specfic PubMed IDs (PMIDs).has PubMed associationhas PubMed associationAn assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.temporal interpretationtemporal interpretationhttps://github.com/oborel/obo-relations/wiki/ROAndTimeAn assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.logical macro assertionlogical macro assertionhttps://github.com/oborel/obo-relations/wiki/ShortcutRelationsA logical macro assertion whose domain is an IRI for a propertylogical macro assertion on a propertylogical macro assertion on a propertyUsed to annotate object properties to describe a logical meta-property or characteristic of the object property.logical macro assertion on an object propertylogical macro assertion on an object propertyUsed to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0"cjm2018-03-13T23:59:29Zis directional form ofcjm2018-03-14T00:03:16Zis positive form ofcjm2018-03-14T00:03:24Zis negative form ofA metadata relation between a class and its taxonomic rank (eg species, family)ncbi_taxonomyThis is an abstract class for use with the NCBI taxonomy to name the depth of the node within the tree. The link between the node term and the rank is only visible if you are using an obo 1.3 aware browser/editor; otherwise this can be ignoredhas_rankhas_rankTypically, Date will be associated with the creation or
availability of the resource. Recommended best practice
for encoding the date value is defined in a profile of
ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.A date associated with an event in the life cycle of the
resource.DateDateDescription may include but is not limited to: an abstract,
table of contents, reference to a graphical representation
of content or a free-text account of the content.An account of the content of the resource.DescriptionDescriptionTypically, a Subject will be expressed as keywords,
key phrases or classification codes that describe a topic
of the resource. Recommended best practice is to select
a value from a controlled vocabulary or formal
classification scheme.The topic of the content of the resource.Subject and KeywordsSubject and Keywords
Typically, a Title will be a name by which the resource is
formally known.
A name given to the resource.TitleTitledescriptionMark Miller2018-05-11T13:47:29Zhas_alternative_idhas_alternative_idhas_broad_synonymdatabase_cross_referencedatabase_cross_referencehas_exact_synonymhas_exact_synonymhas_narrow_synonymhas_narrow_synonymhas_obo_namespacehas_obo_namespacehas_related_synonymhas_related_synonymin_subsetin_subsetlabellabelpart ofpart ofhas parthas partinheres in at all timesrealizesprecedesx precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.precedesoccupies spatial region at some timeMeng LIU (Mia), Oliver Heexists ata has_disposition b at t =Def. b disposition_of a at t. (axiom label in BFO2 Reference: [069-001])Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has disposition at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has disposition@en(x,y,t)'.(iff (hasDispositionAt a b t) (dispositionOf b a t)) // axiom label in BFO2 CLIF: [069-001]has disposition at all timesspecifically depends on at some timehas continuant part at some timehas continuant part at all times that part existsMeng LIU (Mia), Oliver Hehas predicted parta relation between a protein and the organism where this protein belongs to the organism.Meng LIU (Mia), Oliver Heis protein of organismThe organism where the ICE is first identifed from.Meng LIU (Mia), Oliver Heis ICE of organismMeng LIU (Mia), Oliver Hea relation between a sequence and the organism where this sequence belongs to the organism.is sequence of organisma in silico relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existenceMeng LIU (Mia), Oliver Hehas susceptibility rolehas gene participanthas protein participanthas sequence participanthas susceptibility gene participantMeng LIU (Mia), Oliver Hetransferred asthe inverse property of encodesMeng LIU (Mia), Oliver Heencoded_byto specify the genetic code forMeng LIU (Mia), Oliver Heencodesa relation between a gene and the organism where this gene belongs to the organism in nature. It does not include a foreign gene that is transferred to an organism by a genetic engineering method.Oliver He, Yue Liuis gene of organismis gene of organisminheres inbearer ofthis apple is bearer of this red colorthis vase is bearer of this fragilitya relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existenceA bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.bearer_ofis bearer ofbearer ofparticipates inthis blood clot participates in this blood coagulationthis input material (or this output material) participates in this processthis investigator participates in this investigationa relation between a continuant and a process, in which the continuant is somehow involved in the processparticipates_inparticipates inhas participantthis blood coagulation has participant this blood clotthis investigation has participant this investigatorthis process has participant this input material (or this output material)a relation between a process and a continuant, in which the continuant is somehow involved in the processHas_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.has_participanthttp://www.obofoundry.org/ro/#OBO_REL:has_participanthas participantthis person has role this investigator role (more colloquially: this person has this role of investigator)a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existenceA bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.has_rolehas rolehappens duringA is spatially_disjoint_from B if and only if they have no parts in commonThere are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.Chris MungallNote that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchyBFO_0000051 exactly 0 (BFO_0000050 some ?Y)spatially disjoint fromhttps://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Patternprocess(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicitChris MungallDavid HillTanya BerardiniGORegulation precludes parthood; the regulatory process may not be within the regulated process.regulates (processual)falseregulatesProcess(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.Chris Mungallnegatively regulates (process to process)negatively regulatesProcess(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.Chris Mungallpositively regulates (process to process)positively regulatesA caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.The epidermis layer of a vertebrate is adjacent to the dermis.The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.x adjacent to y if and only if x and y share a boundary.This relation acts as a join point with BSPOChris Mungalladjacent toChris MungallDo not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.temporally related toMeng LIU (Mia), Oliver Heends withcjmholds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of ycausally upstream of, positive effectcjmholds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of ycausally upstream of, negative effectA mereological relationship or a topological relationshipChris MungallDo not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationshipsmereotopologically related toregulated bynegatively regulated bypositively regulated byThis relation groups causal relations between material entities and causal relations between processesThis branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.
To define causal relations in an activity-flow type network, we make use of 3 primitives:
* Temporal: how do the intervals of the two occurrents relate?
* Is the causal relation regulatory?
* Is the influence positive or negative
The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.
For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.
For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.
Each of these 3 primitives can be composed to yield a cross-product of different relation types.Chris MungallDo not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.causally related top is causally upstream of q if and only if p precedes q and p and q are linked in a causal chainChris Mungallcausally upstream ofp 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2Chris Mungallinfluences (processual)affectscausally upstream of or withincausally downstream of or withinp is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.Chris MungallDo not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.causal relation between processesdirectly regulatescjm2018-03-13T23:55:05Zcausally upstream of or within, negative effectcjm2018-03-13T23:55:19Zcausally upstream of or within, positive effectClusters of antibiotic resistance genes. May be regulated by a shared promoter or repressor.antibiotic_resistanceARO:0000010antibiotic resistance gene cluster, cassette, or operonentityEntityJulius CaesarVerdi’s Requiemthe Second World Waryour body mass indexBFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdfAn entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])entitycontinuantContinuantBFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuantsA continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002](forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001](forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002](forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]continuantoccurrentOccurrentBFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial regionBFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001](forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]occurrenticIndependentContinuanta chaira hearta lega moleculea spatial regionan atoman orchestra.an organismthe bottom right portion of a human torsothe interior of your mouthb is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001](forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002](iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]independent continuantspatial regiontemporal regionprocessProcessa process of cell-division, \ a beating of the hearta process of meiosisa process of sleepingthe course of a diseasethe flight of a birdthe life of an organismyour process of aging.p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]processdispositionDispositionan atom of element X has the disposition to decay to an atom of element Ycertain people have a predisposition to colon cancerchildren are innately disposed to categorize objects in certain ways.the cell wall is disposed to filter chemicals in endocitosis and exocitosisthe cell wall is disposed to filter chemicals in endocytosis and exocytosisBFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type [89BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002](forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]dispositionrealizableRealizableEntitythe disposition of this piece of metal to conduct electricity.the disposition of your blood to coagulatethe function of your reproductive organsthe role of being a doctorthe role of this boundary to delineate where Utah and Colorado meetTo say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002](forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]realizable entityqualityQualitythe ambient temperature of this portion of airthe color of a tomatothe length of the circumference of your waistthe mass of this piece of gold.the shape of your nosethe shape of your nostrila quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001](forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]qualitysdcSpecificallyDependentContinuantReciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this keyof one-sided specifically dependent continuants: the mass of this tomatoof relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.the disposition of this fish to decaythe function of this heart: to pump bloodthe mutual dependence of proton donors and acceptors in chemical reactions [79the mutual dependence of the role predator and the role prey as played by two organisms in a given interactionthe pink color of a medium rare piece of grilled filet mignon at its centerthe role of being a doctorthe shape of this hole.the smell of this portion of mozzarellab is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004](iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]specifically dependent continuantroleRoleJohn’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.the priest rolethe role of a boundary to demarcate two neighboring administrative territoriesthe role of a building in serving as a military targetthe role of a stone in marking a property boundarythe role of subject in a clinical trialthe student roleBFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]rolethree-dimensional spatial regionbfoBFO:0000030objectgdcGenericallyDependentContinuantThe entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.the pdf file on your laptop, the pdf file that is a copy thereof on my laptopthe sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]generically dependent continuantfunctionFunctionthe function of a hammer to drive in nailsthe function of a heart pacemaker to regulate the beating of a heart through electricitythe function of amylase in saliva to break down starch into sugarBFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]functionmaterialMaterialEntitya flamea forest firea human beinga hurricanea photona puff of smokea sea wavea tornadoan aggregate of human beings.an energy wavean epidemicthe undetached arm of a human beingBFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002](forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002](forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]bfoBFO:0000040material entitymaterial entityimmaterialImmaterialEntityBFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10immaterial entityAny constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.chebi_ontologyCHEBI:23367molecular entityA chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.chebi_ontologyCHEBI:24431chemical entityA compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups.chebi_ontologyCHEBI:50047organic amino compoundThe removal of the oligonucleotide that contains the DNA damage. The oligonucleotide is formed by dual incisions that flank the site of DNA damage.biological_processGO:0000718nucleotide-excision repair, DNA damage removalThe union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms.Wikipedia:Conjugationbiological_processGO:0000746conjugationThe cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.GO:0055133MIPS_funcat:10.01.03Wikipedia:DNA_replicationbiological_processGO:0006260DNA biosynthesis is only part of this process. See also the biological process terms 'DNA-dependent DNA replication ; GO:0006261' and 'RNA-dependent DNA replication ; GO:0006278'.DNA replicationA biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.janelomax2012-09-19T15:05:24ZGO:0000004GO:0007582GO:0044699Wikipedia:Biological_processbiological processphysiological processbiological_processsingle organism processsingle-organism processGO:0008150Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this.biological_processCatalysis of the integration of one segment of DNA into another.Reactome:R-HSA-164523molecular_functionGO:0008907integrase activityCatalysis of the formation of new phosphodiester bonds between a pair of short, unique DNA target sequences; occurs through a phosphotyrosyl intermediate in which the target sequence is first cleaved by the nucleophilic attack by a tyrosine in the active site.tyrosine recombinasesite-specific tyrosine recombinase activitymolecular_functionGO:0009037tyrosine-based site-specific recombinase activityThe process in which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.MIPS_funcat:10.01.05.03.05biological_processGO:0015074DNA integrationThe removal of a section of DNA from a larger DNA molecule by the making of dual incisions that flank the section to be excised.janelomax2011-08-03T10:56:37Zbiological_processGO:0044349DNA excisionAny process that modulates a measurable attribute of any biological process, quality or function.regulationbiological_processGO:0065007biological regulationA DNA-dependent DNA replication process in which a single-stranded DNA molecule is synthesized from a circular duplex template. Replication typically does not cease when one circumference has been replicated, but continues around the circumference several more times, producing a long single strand comprising multimers of the replicon.midori2009-04-22T02:53:52Zrolling circle replicationbiological_processGO:0070581rolling circle DNA replicationA bacterial protein complex that neutralises its own toxin by complexing the toxin with the antitoxin. The antitoxin can be either a protein or an RNA. The neutralising toxin-antitoxin complex also acts as a transcriptional repressor of the toxin-antitoxin operon.toxin-antitoxin systemkmvIntAct:EBI-10919614IntAct:EBI-13949147IntAct:EBI-13949218IntAct:EBI-13949593IntAct:EBI-13949715IntAct:EBI-13949851cellular_componentGO:0110001An example is YoeB (P69348) in Escherichia coli in PMID:16109374 (inferred by direct evidence).toxin-antitoxin complexhighly modular mobile genetic element, which has both plasmid-and bacteriophage-like features, encodes gene and proteins for its excision, its transfer by conjugation and its integration.Meng LIU (Mia), Oliver HeICEhttp://db-mml.sjtu.edu.cn/ICEberg/integrative and conjugative elementPseudomonas aeruginosa PSE9Pseudomonas syringae pv. phaseolicola 1302AThe SXT/R391 family was defined by <a href="http://www.ncbi.nlm.nih.gov/pubmed/16530834">Burrus et al (2006)</a>.They proposed that any ICE that encodes an integrase gene closely related to<em> int</em>SXT and that integrates into <em>prfC</em> be considered part of the SXT/R391 family of ICEs. In addition the tra genes, which encode the ICE conjugation apparatus, are also a defining feature of this family of ICEs. However, there are some exceptions for those that share a syntenic ‘core’ structure and features but have a different integraseMeng LIU (Mia), Oliver HeICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/SXT/R391 family ICEMeng LIU (Mia), Oliver He40http://202.120.12.136/ICEberg2/feature_page.php?ice_id=4080.6 kbAM94275946.73[38.9]2649499..2730130ICE with experimental supportprfC (PMI2422)ICEPmiUSA1Meng LIU (Mia), Oliver He39http://202.120.12.136/ICEberg2/feature_page.php?ice_id=39111.2 kbShewanella putrefaciensCP00050348.28[44.63]1224492..1335682ICE with experimental supportprfC (Sputw3181_1184)ICESpuPO1Meng LIU (Mia), Oliver He16http://202.120.12.136/ICEberg2/feature_page.php?ice_id=16107.7 kbCP00148536.42958347..3066049ICE with experimental supportprfC (VCD_003660)ICEVchBan9Meng LIU (Mia), Oliver He12http://202.120.12.136/ICEberg2/feature_page.php?ice_id=12102.1 kbBacteroides spp.GQ46314047.281..102122ICE with experimental supportprfCICEVchBan5Meng LIU (Mia), Oliver He22http://202.120.12.136/ICEberg2/feature_page.php?ice_id=2298 kbGQ46314246.731..97952ICE with experimental supportprfCICEVchInd5 [ICEVchHai1]Meng LIU (Mia), Oliver He23http://202.120.12.136/ICEberg2/feature_page.php?ice_id=2383.2 kbGQ46314346.731..83194ICE with experimental supportprfCICEVchMex1Meng LIU (Mia), Oliver He21http://202.120.12.136/ICEberg2/feature_page.php?ice_id=2195.3 kbGQ46314146.871..95326ICE with experimental supportprfCICEVchInd4Meng LIU (Mia), Oliver He36http://202.120.12.136/ICEberg2/feature_page.php?ice_id=36114.2 kbGQ46314447.591..114195ICE with experimental supportprfCICEVflInd1Meng LIU (Mia), Oliver He37http://202.120.12.136/ICEberg2/feature_page.php?ice_id=3796.7 kbGQ46313947.091..96676ICE with experimental supportprfCICEPalBan1Meng LIU (Mia), Oliver He38http://202.120.12.136/ICEberg2/feature_page.php?ice_id=38103 kbEscherichia coliAJ87098646.341..102985ICE with experimental supportprfCICEPdaSpa1Meng LIU (Mia), Oliver He43http://202.120.12.136/ICEberg2/feature_page.php?ice_id=4388.5 kbEscherichia coli; Bacteroides spp.AY09055946.481..88532ICE with experimental supportprfCR391Meng LIU (Mia), Oliver He44http://202.120.12.136/ICEberg2/feature_page.php?ice_id=4499.5 kbVibrio cholerae; Escherichia coli; Salmonella enterica serovar TyphimuriumAY05542847.051..99483ICE with experimental supportprfCResistance to the antibiotics sulfamethoxazole, trimethoprim, chloramphenicol, and streptomycin; Toxin-Antitoxin SystemSXT(MO10)Meng LIU (Mia), Oliver He1016http://202.120.12.136/ICEberg2/feature_page.php?ice_id=101692.8 kbEscherichia coli48.01ICE with experimental supportprfCICEPmiChn1Escherichia coli ECOR31Meng LIU (Mia), Oliver He200013http://202.120.12.135/oriTDB/browse_oriT_result.php?acc=200013250 ntintactexperimental17981959oriT_ ICEKp1ICEKp1 AMThe set of gene and non-gene sequence responsible for the DNA integration process in the integration and excision module of ICE ICEKp1.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEKp1 IEM for integrationICEKp1 RMgene that encodes a protein which nicks the dsDNA and remains covalently bound to the resulting ssDNAMeng LIU (Mia), Oliver Hehttps://en.wikipedia.org/wiki/Relaxaserelaxase geneA role played by gene that encodes a protein which has the ability to neutralize a specific toxin.Meng LIU (Mia), Oliver Heantitoxin gene roleA role played by a material entity that has the ability to neutralize a specific toxin.Meng LIU (Mia), Oliver Hehttps://en.wikipedia.org/wiki/Antitoxinantitoxin roleMeng LIU (Mia), Oliver HeT4SS gene componenttype IV secretion system gene componentA relaxase is a single-strand DNA transesterase enzyme produced by some prokaryotes and viruses, which nicks the dsDNA and remains covalently bound to the resulting ssDNA. Relaxases are responsible for site- and strand-specific nicks in double-stranded DNA.Meng LIU (Mia), Oliver HeMOBhttps://en.wikipedia.org/wiki/RelaxaserelaxaseA role played by gene that encodes a protein which is poisonous.Meng LIU (Mia), Oliver Hetoxin gene roleMeng LIU (Mia), Oliver Herecombinase genegene encoding products that mediate an exchange reaction between two DNA templates, resulting in integration of DNA from one of the templates into the other.integrase genea protein component of T4SSMeng LIU (Mia), Oliver HeT4SS protein componenthttps://academic.oup.com/nar/article/47/D1/D660/5165266type IV secretion system protein componentA role played by a protein which is part of T4SS (a cell envelope-spanning complexes that form a channel through which DNA and proteins can travel from the cytoplasm of the donor cell to the cytoplasm of the recipient cell. )Meng LIU (Mia), Oliver HeT4SS protein component roletype IV secretion system protein component roleA role played by a gene that encodes products to mediate an exchange reaction between two DNA templates and result in integration of DNA from one of the templates into the other.Meng LIU (Mia), Oliver Heintegrase gene rolegene that encodes a transposase enzyme with the DDE motif.Meng LIU (Mia), Oliver Hehttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2991504/DDE transposase genegene encoding one family of recombinases that use serine to attack and covalently link the DNA during strand exchange.Meng LIU (Mia), Oliver Hehttps://en.wikipedia.org/wiki/Site-specific_recombinationserine recombinase genegene encoding one family of recombinases that use tyrosine to attack and covalently link the DNA during strand exchange.Meng LIU (Mia), Oliver Hehttps://en.wikipedia.org/wiki/Site-specific_recombinationtyrosine recombinase geneMeng LIU (Mia), Oliver HeThe set of gene and non-gene sequence responsible for the DNA excision process in the integration and excision module of ICE ICEKp1.http://db-mml.sjtu.edu.cn/ICEberg/ICEKp1 IEM for excisionthe integration and excision module of ICE ICEKp1.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEKp1 IEMThe integration and excision module refers to those genes and sequence within the ICE responsible for the integration and excision of the element from the host chromosome, including genes encoding the integrase and or recombination directionality factor (also known as excisionase, which influences the direction of recombination mediated by the integrase to favor excision).Meng LIU (Mia), Oliver Herecombination module componenthttps://academic.oup.com/nar/article/47/D1/D660/5165266ICE IEM for integrationA role played by a gene that encodes a protein for nicking the dsDNA.Meng LIU (Mia), Oliver Herelaxase gene roleA role played by a gene that encodes products for controlling the directionality of integrase-mediated site-specific recombination reactions.Meng LIU (Mia), Oliver HeRDF gene rolerecombination directionality factor gene roleGene encoding products that involved in controlling the directionality of integrase-mediated site-specific recombination reactions.Meng LIU (Mia), Oliver HeRDF genehttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC55702/recombination directionality factor genegene encoding products that link translocating substrates to the transenvelope secretion conduit.Meng LIU (Mia), Oliver Hegene of T4CPhttps://www.nature.com/articles/nmicrobiol2017114gene of type IV coupling proteinMeng LIU (Mia), Oliver Hegene of T4CP rolea role played by a gene that encodes a protein which links translocating substrates to the transenvelope secretion conduit.gene of type IV coupling protein rolea role played by a gene that encodes a protein for energizing the T4SS system from the cytoplasm and driving the complex assembly and substrate translocation through the channel.Meng LIU (Mia), Oliver HeT4SS ATPase gene roleMeng LIU (Mia), Oliver Hegene of T4SS ATPaseA role played by a material entity that contributes to the integration and excision of the element from the host chromosome.Meng LIU (Mia), Oliver Heintegration and excision module component roleThe integration and excision module refers to those genes and sequence within the ICE responsible for the integration and excision of the element from the host chromosome, including genes encoding the integrase and or recombination directionality factor (also known as excisionase, which influences the direction of recombination mediated by the integrase to favor excision).Meng LIU (Mia), Oliver Herecombination module componenthttps://academic.oup.com/nar/article/47/D1/D660/5165266ICE IEM for excisionThe Tn<em>4371</em> family was defined by <a href="http://www.ncbi.nlm.nih.gov/pubmed/19941653">Ryan et al (2009)</a>. propose that\n any ICE that encodes an integrase gene closely related to \n <em>int</em>Tn<em>4371</em>, defined as over 70% protein homology and that \n has similar maintenance and transfer genes be considered \npart of the Tn<em>4371</em> family of ICEs. However, we lessen the protein homology to 60% for those similar in sequence.Meng LIU (Mia), Oliver HeICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/Tn4371 family ICEThe CTnDOT/ERL family was described in <a href="http://www.ncbi.nlm.nih.gov/pubmed/19941653">Whittle et al (2002)</a>. We classified any ICE that encodes an integrase gene closely related to <em> intDOT</em>, defined as over 60% protein homology and that that has significant sequence alignment and syntenic 'core' structure in the CTnDOT/ERL family of ICEs.Meng LIU (Mia), Oliver HeICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/CTnDOT/ERL family ICEICE<em>clc</em>(B13) is a well studied ICE. We selected it as a reference and defined ICE<em>clc </em> family. We classified any ICE that encodes an integrase gene closely related to <em> intB13</em>;, defined as over 60% protein homology and that has significant sequence \nalignment and syntenic 'core' structure into the ICE<em>clc </em>family.Meng LIU (Mia), Oliver HeICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/ICEclc family ICEICE<em>Bs1</em> is a well studied ICE. We selected it as a reference and defined <em>ICE<em>Bs1</em> </em>family. We classified any ICE that encodes an integrase gene closely related to <em>int</em>(ICE<em>Bs1)</em>, defined as over 60% protein homology and that has significant sequence alignment and syntenic 'core' structure into the ICE<em>clc </em>family.Meng LIU (Mia), Oliver HeICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/ICEBs1 family ICEICE<em>Hin</em>1056 is a well studied ICE. We selected it as a reference and difined ICE<em>Hin</em>1056 family. We classified any ICE that encodes an integrase gene closely related to <em>int</em>(<em>ICE<em>Hin</em>1056)</em>, defined as over 60% protein homology and that that has significant sequence alignment and syntenic 'core' structure into the ICE<em>Hin</em>1056 family.Meng LIU (Mia), Oliver HeICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/ICEHin1056 family ICEPAPI-1 is a well studied ICE. We selected it as a reference and defined PAPI-1 family. We classified any ICE that encodes an integrase gene closely related to <em>int</em>(<em>PAPI-1)</em>, defined as over 60% protein homology and that that has significant sequence alignment and syntenic 'core' structure into the PAPI-1 family.Meng LIU (Mia), Oliver HeICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/PAPI-1 family ICEICE<em>Ml</em>Sym(R7A) is a well studied ICE. We classified ICE that that has significant sequence alignment and syntenic 'core' structure with ICE<em>Ml</em>Sym(R7A) into the ICE<em>Ml</em>Sym(R7A) family.Meng LIU (Mia), Oliver HeICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/ICEMlSym(R7A) family ICEICE<em>St1</em> is a well studied ICE. We selected it as a reference and defined ICE<em>St1</em> family. We classified any ICE that encodes an integrase gene closely related to <em>int</em>(<em>ICE<em>St1</em>) </em>or <em>int(ICESpn8140)</em>, defined as over 60% protein homology and that that has significant sequence alignment and syntenic 'core' structure into the ICE<em>St1</em> family.Meng LIU (Mia), Oliver HeICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/ICESt1 family ICESPI-7 is a well studied ICE. We selected it as a reference and defined SPI-7 family. We classified any ICE that encodes an integrase gene closely related to <em>int(SPI-7)</em>, defined as over 60% protein homology and that that has significant sequence alignment and syntenic 'core' structure into the this <em></em> family.Meng LIU (Mia), Oliver HeICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/SPI-7 family ICEICE<em>6013</em> was characterized by <a href="http://www.ncbi.nlm.nih.gov/pubmed/19648240">Smyth et al</a>. ICEs in ICE<em>6013</em> family are defined by the following structure based on the figure from Smyth et al.<br />\n<img src="images/ICE6013.png" width="620" height="183" border="0" align="middle" />Meng LIU (Mia), Oliver HeICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/ICE6013 family ICEWe classified ICE that has significant sequence alignment and syntenic 'core' structure with Tn<em>GBS1</em> into the Tn<em>GBS1</em> family.Meng LIU (Mia), Oliver HeICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/TnGBS1 family ICETn<em>5253</em> is a composite structure of two conjugative transposons, Tn<em>5251</em> and Tn<em>5252</em>. We selected it as a reference and defined Tn<em>5253</em> family. We classified ICE that has significant sequence alignment and syntenic 'core' structure with Tn<em>5253</em> into the Tn<em>5253</em> family, including Tn<em>5252</em> and Tn<em>5252</em>-like ICEs.Meng LIU (Mia), Oliver HeICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/Tn5253 family ICEICE<em>Sa</em>2603 is a well studied ICE. We selected it as a reference and defined ICE<em>Sa</em>2603 family. We classified any ICE that encodes an integrase gene closely related to <em>int(ICE<em>Sa</em>2603)</em>, defined as over 60% protein homology and that has significant sequence alignment and syntenic 'core' structure into the this <em></em> family.Meng LIU (Mia), Oliver HeICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/ICESa2603 family ICEWe selected ICE<em>Ye1</em> as a reference and defined ICE<em>Ye1</em> family. We classified any ICE that encodes an integrase gene closely related to <em>int(ICE<em>Ye1</em>)</em>, defined as over 60% protein homology and that has significant sequence alignment and syntenic 'core' structure into the this family.Meng LIU (Mia), Oliver HeICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/ICEYe1 family ICEWe selected 10270-RD.2 as a reference and defined 10270-RD.2 family. We calssified ICE that has significant sequence alignment and syntenic 'core' structure with 10270-RD.2 into this family.Meng LIU (Mia), Oliver HeICEberg2 databasehttp://db-mml.sjtu.edu.cn/ICEberg/10270-RD.2 family ICEWe selected Tn<em>1207.3</em> as a reference and defined Tn<em>1207.3</em> family. We calssified ICE that has significant sequence alignment and syntenic 'core' structure with Tn<em>1207.3</em> into this family.Meng LIU (Mia), Oliver HeICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/Tn1207.3 family ICEWe selected Tn<em>1806</em> as a reference and defined Tn<em>1806</em> family. We classified ICE that has significant sequence alignment and syntenic 'core' structure with Tn<em>1806</em> into this family.Meng LIU (Mia), Oliver HeICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/Tn1806 family ICEICEA(5632)-I is a well studied ICE. We selected ICEA(5632)-I as a reference and defined ICEA5632 family. We classified ICE that has significant sequence alignment and syntenic 'core' structure with ICEA(5632)-I into the this family.Meng LIU (Mia), Oliver HeICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/ICEA5632 family ICEICEF-I is a well studied ICE. We selected ICEF-I as a reference and defined ICEF-I/II family. We classified ICE that has sequence samilarity with ICEF-I into this family.Meng LIU (Mia), Oliver HeICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/ICEF-I/II family ICEWe selected ICEA(PG2) as a reference and defined ICEA(PG2) family. We calssified ICE that has significant sequence alignment and syntenic 'core' structure with ICEA(PG2) into this family.Meng LIU (Mia), Oliver HeICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/ICEAPG2 family ICEWe selected ICEM as a reference and defined ICEM family. We classified ICE that has significant sequence alignment and syntenic 'core' structure with ICEM into this family.ICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/ICEM family ICEAn enzyme that mediates an exchange reaction between two DNA templates, resulting in integration of DNA from one of the templates into the other.Meng LIU (Mia), Oliver HeIntrecombinasehttps://jb.asm.org/content/185/17/5045integraseWe selected 10270-RD.1 as a reference and defined 10270-RD.1 family. We classified ICE that has significant sequence alignment and syntenic 'core' structure with 10270-RD.1 into this family.Meng LIU (Mia), Oliver HeICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/10270-RD.1 family ICEWe selected Tn<em>5801</em> as a reference and defined Tn<em>5801</em> family. We classified ICE that has significant sequence alignment and syntenic 'core' structure with Tn<em>5801</em> into this family.Meng LIU (Mia), Oliver HeICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/Tn5801 family ICEWe selected Sp23F_PPI-1 as a reference and defined PPI-1 family. We classified ICE that has significant sequence alignment and syntenic 'core' structure with Sp23F_PPI-1 into the this family.Meng LIU (Mia), Oliver HeICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/PPI-1 family ICEWe selected ICEF-IIIA1(M64) as a reference and defined ICEF-III family. We classified ICE that has significant sequence alignment and syntenic 'core' structure with ICEF-IIIA1(M64) into this family.Meng LIU (Mia), Oliver HeICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/ICEF-III family ICEMeng LIU (Mia), Oliver He46http://202.120.12.136/ICEberg2/feature_page.php?ice_id=4654.7 kbCupriavidus metalliduransAJ53675663.491..54657ICE with experimental supportTTTTTCATTn4371Accessory module component refers to genes such as virulence factor (VF) genes and acquired antibiotic resistance genes (ARG) that often exist inside ICEs as the cargo genes and can confer the hosts with selective advantages, which make ICEs a vital role in the process of bacterial adaptation and evolution.Meng LIU (Mia), Oliver Hehttps://academic.oup.com/nar/article/47/D1/D660/5165266ICE accessory moduleMeng LIU (Mia), Oliver He166http://202.120.12.136/ICEberg2/feature_page.php?ice_id=16661.8 kbAB54627063.971..61807ICE with experimental supportICE-KKSMeng LIU (Mia), Oliver He2http://202.120.12.136/ICEberg2/feature_page.php?ice_id=252 kbBacteroides spp.AY51526349.491..51993ICE with experimental supportCTn341Meng LIU (Mia), Oliver He219http://202.120.12.136/ICEberg2/feature_page.php?ice_id=219255.5 kbAM90271661.73[65.48]1083989..1339502ICE with experimental supporttRNA-Gly (tRNA-10)ICE-GI1gene encoding products that can confer the the ability of bacteria and other microorganisms to resist the effects of an antibiotic to which they were once sensitive.Meng LIU (Mia), Oliver Hehttps://www.medicinenet.com/script/main/art.asp?articlekey=2276Antibiotic resistance is a major concern of overuse of antibiotics.antibiotic resistance geneMeng LIU (Mia), Oliver He220http://202.120.12.136/ICEberg2/feature_page.php?ice_id=220143.4 kbAM90271660.59[65.48]1350129..1493558ICE with experimental supportICE-GI2Meng LIU (Mia), Oliver He221http://202.120.12.136/ICEberg2/feature_page.php?ice_id=221102.1 kbAM90271663.02[65.48]1493541..1595651ICE with experimental supporttRNA-Gly (tRNA-11)ICE-GI3Meng LIU (Mia), Oliver He222http://202.120.12.136/ICEberg2/feature_page.php?ice_id=222159.1 kbAM90271661.15[65.48]4417743..4576839ICE with experimental supporttRNA-Gly (tRNA-44)ICE-GI6Meng LIU (Mia), Oliver Hegene encoding products that assist the bacterium colonize the host at the cellular level and are either secretory, membrane associated or cytosolic in nature.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5243249/virulence factor geneThe conjugation module denotes those genes and sequences involved in the conjugal process, such as genes encoding relaxase and the type IV secretion system (T4SS).Meng LIU (Mia), Oliver Hehttps://academic.oup.com/nar/article/47/D1/D660/5165266ICE conjugation moduleMeng LIU (Mia), Oliver He56http://202.120.12.136/ICEberg2/feature_page.php?ice_id=56102.8 kbPseudomonas putida; Pseudomonas aeruginosa; Cupriavidus necatorAJ61774062.5160..102843ICE with experimental supporttRNA-GlyICEclc(B13)Meng LIU (Mia), Oliver He174http://202.120.12.136/ICEberg2/feature_page.php?ice_id=174105 kbAF44052364.7127286..132240ICE with experimental supporttRNA-GlyPAGI-2Meng LIU (Mia), Oliver He1077http://202.120.12.136/ICEberg2/feature_page.php?ice_id=1077173.8 kbAzoarcus sp. CIBTRifCP0110724894159..5067957ICE with experimental supporttRNAGly(TTCGATTCCCATCGCCCGCTCCA)ICEXTDMeng LIU (Mia), Oliver He1010http://202.120.12.136/ICEberg2/feature_page.php?ice_id=101086.2 kbPseudomonas aeruginosaKY85237563.05315..86517ICE with experimental supporttRNAGlyICEPae690Meng LIU (Mia), Oliver He59http://202.120.12.136/ICEberg2/feature_page.php?ice_id=5920.5 kbBacillus and Listeria speciesAL00912635.7[43.51]529423..549932ICE with experimental supporttRNA-Leu(BSU_tRNA_51)ICEBs1Meng LIU (Mia), Oliver He60http://202.120.12.136/ICEberg2/feature_page.php?ice_id=6059.4 kbHaemophilus influenzae; Haemophilus parainfluenzaeAJ62738639.11..59393ICE with experimental supporttRNA-LeuICEHin1056Meng LIU (Mia), Oliver He960http://202.120.12.136/ICEberg2/feature_page.php?ice_id=96056.1 kbActinobacillus pleuropneumoniaeKU55130927..56176ICE with experimental supporttRNA-Leu (TAA)ICEApl1Meng LIU (Mia), Oliver He175http://202.120.12.136/ICEberg2/feature_page.php?ice_id=175108 kbCP00043859.74[66.29]5251440..5359392ICE with experimental supporttRNA-Lys (Lys47)PAPI-1Meng LIU (Mia), Oliver He173http://202.120.12.136/ICEberg2/feature_page.php?ice_id=173103.5 kbAY25753860.931..103532ICE with experimental supporttRNA-LyspKLC102Meng LIU (Mia), Oliver He176http://202.120.12.136/ICEberg2/feature_page.php?ice_id=17699.3 kbEF61130159.621..99276ICE with experimental supporttRNA-Lys (Lys47)PAGI-5Meng LIU (Mia), Oliver He78http://202.120.12.136/ICEberg2/feature_page.php?ice_id=7835.9 kbAJ27847134.991290..36049ICE with experimental supportfdaICESt1Meng LIU (Mia), Oliver He79http://202.120.12.136/ICEberg2/feature_page.php?ice_id=7928.1 kbStreptococcus pyogenes; Enterococcus faecalisAJ58656836.9204..28293ICE with experimental supportfdaICESt3Meng LIU (Mia), Oliver He288http://202.120.12.136/ICEberg2/feature_page.php?ice_id=288133.5 kbAL51338249.68[52.09]4409574..4543073ICE with experimental supporttRNA-PheUSPI-7Meng LIU (Mia), Oliver He113http://202.120.12.136/ICEberg2/feature_page.php?ice_id=113109.4 kbFN29849451.021785..111202ICE with experimental supporttRNA-PheICESb1Meng LIU (Mia), Oliver He358http://202.120.12.136/ICEberg2/feature_page.php?ice_id=35813.3 kbAB43501430.14928..14266ICE with experimental supportTn6012Meng LIU (Mia), Oliver He68http://202.120.12.136/ICEberg2/feature_page.php?ice_id=6819.9 kbStaphylococcus aureusFJ23127029.621..19905ICE with experimental supportICE6013Meng LIU (Mia), Oliver He160http://202.120.12.136/ICEberg2/feature_page.php?ice_id=16047.1 kbNC_00436837.66[35.63]385757..432824ICE with experimental supportTnGBS1Meng LIU (Mia), Oliver He165http://202.120.12.136/ICEberg2/feature_page.php?ice_id=16561 kbFR67034733.181..61030ICE with experimental supportICE6094Meng LIU (Mia), Oliver He377http://202.120.12.136/ICEberg2/feature_page.php?ice_id=37754.3 kbAE00994838.35[35.65]1256680..1311028ICE with experimental supportICESa2603Meng LIU (Mia), Oliver He311http://202.120.12.136/ICEberg2/feature_page.php?ice_id=31188.9 kbCP00040738.79[41.11]872967..961817ICE with experimental supportTTATTTAAGAGTAACICESsu05ZYH33-1Meng LIU (Mia), Oliver He76http://202.120.12.136/ICEberg2/feature_page.php?ice_id=7663.7 kbHemolytic StreptococciEU14204138.141..63668ICE with experimental supportICESde3396Meng LIU (Mia), Oliver He445http://202.120.12.136/ICEberg2/feature_page.php?ice_id=44554.9 kbStreptococcus suis v36RF; Streptococcus pyogenes 12RF; Streptococcus pneumoniae R6RF; Streptococcus agalactiae 1357RFFR82330438.891..54879ICE with experimental supportTTATTTAAGAGTAACICESsu32457Meng LIU (Mia), Oliver He791http://202.120.12.136/ICEberg2/feature_page.php?ice_id=79173.4 kbStreptococcus agalactiaeStreptococcus pneumoniae; Streptococcus gordonii; Streptococcus pyogenes; Streptococcus agalactiae;Enterococcus faecalis; Bacillus subtilisCP01997837.73629058..702486ICE with experimental supportrumAICESag37Meng LIU (Mia), Oliver Heprotein of Bacteriaa typical class of ICEs which transfer as single stranded DNA molecules and require T4SS and can both found in Gram-positive bacteria and Gram-negative bacteriaMeng LIU (Mia), Oliver HeT4SS-type ICEhttp://db-mml.sjtu.edu.cn/ICEberg/T4SS-type integrative and conjugative elementa T4SS-type ICE of Gram-positive bacteriaMeng LIU (Mia), Oliver HeT4SS-type ICE in Gram-positive bacteriahttp://db-mml.sjtu.edu.cn/ICEberg/T4SS-type integrative and conjugative element in Gram-positive bacteriaa T4SS-type ICE of Gram-negative bacteriaMeng LIU (Mia), Oliver HeT4SS-type ICE in Gram-negative bacteriahttp://db-mml.sjtu.edu.cn/ICEberg/T4SS-type integrative and conjugative element in Gram-negative bacteriaICE<em>Kp1</em> is a well studied ICE. We selected it as a reference and defined ICE<em>Kp1</em> family. We classified any ICE that encodes an integrase gene closely related to <em>int(ICE<em>Kp1</em>)</em>, defined as over 60% protein homology and that has significant sequence alignment and syntenic 'core' structure into the this <em></em> family.ICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/ICEKp1 family ICEMeng LIU (Mia), Oliver He70http://202.120.12.136/ICEberg2/feature_page.php?ice_id=7038.9 kbEscherichia coliAY23333347.731..38927ICE with experimental supporttRNA-AsnICEEc1126http://202.120.12.136/ICEberg2/feature_page.php?ice_id=12675935Klebsiella pneumoniae;Escherichia coli3: complete in a genome fileAP00672552.18[57.68]3395836..34717701: experimentalpredicted to mobilize GIE492 in transtRNA-asn(KP1_6086)19447910; 17981959ICEKp1Meng LIU (Mia), Oliver He961http://202.120.12.136/ICEberg2/feature_page.php?ice_id=96192.7 kbActinobacillus pleuropneumoniaeMF18796546.941..92660ICE with experimental supportprfCICEApl2Meng LIU (Mia), Oliver He1017http://202.120.12.136/ICEberg2/feature_page.php?ice_id=101799.4 kbKX24340446.981..99355ICE with experimental supportICEPmiCHN1586Meng LIU (Mia), Oliver He1020http://202.120.12.136/ICEberg2/feature_page.php?ice_id=102097.1 kbKX24340547.031..97078ICE with experimental supportICEPmiCHN2407Meng LIU (Mia), Oliver He1028http://202.120.12.136/ICEberg2/feature_page.php?ice_id=102890.6 kbEscherichia coli J53KY43772847.541..90566ICE with experimental supportICEPmiChn4Meng LIU (Mia), Oliver He1019http://202.120.12.136/ICEberg2/feature_page.php?ice_id=1019104.4 kbEscherichia coli J53KY43772647.341..104371ICE with experimental supportICEPmiChn2Meng LIU (Mia), Oliver He1018http://202.120.12.136/ICEberg2/feature_page.php?ice_id=101876.2 kbKX24341347.111..76218ICE with experimental supportICEPmiCHN1809Meng LIU (Mia), Oliver He1027http://202.120.12.136/ICEberg2/feature_page.php?ice_id=102790 kbKX24341647.771..89996ICE with experimental supportICEPmiCHN3335a special class of ICEs, which have the ability to replicate autonomously like a plasmid, transfer as double stranded circular DNA molecules and do not require a genuine T4SS and are only found in Actinobacteria.Meng LIU (Mia), Oliver HeAICEhttp://db-mml.sjtu.edu.cn/ICEberg/actinomycete integrative and conjugative elementMeng LIU (Mia), Oliver Heprotein of KlebsiellaMeng LIU (Mia), Oliver Heprotein of Klebsiella pneumoniae NTUH-K2044Meng LIU (Mia), Oliver He827http://202.120.12.136/ICEberg2/feature_page.php?ice_id=82755.3 kbStreptococcus pyogenes; Streptococcus pneumoniaeKU05670139.561..55259ICE with experimental supportICESpy009Meng LIU (Mia), Oliver He406http://202.120.12.136/ICEberg2/feature_page.php?ice_id=40698.1 kbAJ62738847.781402..99513ICE with experimental supporttRNA-PheYAPIMeng LIU (Mia), Oliver He172http://202.120.12.136/ICEberg2/feature_page.php?ice_id=17252.5 kbMycoplasma agalactiaeAY65700239.151..52491ICE with experimental supportTn1207.3Meng LIU (Mia), Oliver He409http://202.120.12.136/ICEberg2/feature_page.php?ice_id=40945.5 kbFR69105431.071694..47149ICE with experimental support3' end of the rum geneICESp1108Meng LIU (Mia), Oliver He69http://202.120.12.136/ICEberg2/feature_page.php?ice_id=6927.2 kbMycoplasma agalactiaeFP67113827.37[29.62]813253..840487ICE with experimental supportICEA(5632)-IMeng LIU (Mia), Oliver He225http://202.120.12.136/ICEberg2/feature_page.php?ice_id=22527.2 kbFP67113827.39[29.62]343591..370761ICE with experimental supportICEA(5632)-IIMeng LIU (Mia), Oliver He226http://202.120.12.136/ICEberg2/feature_page.php?ice_id=22627.2 kbFP67113827.37[29.62]560640..587874ICE with experimental supportICEA(5632)-IIIMeng LIU (Mia), Oliver He72http://202.120.12.136/ICEberg2/feature_page.php?ice_id=7223.8 kbAY16895328.632674..26451ICE with experimental supportpdhA, orf251ICEF-IMeng LIU (Mia), Oliver He224http://202.120.12.136/ICEberg2/feature_page.php?ice_id=22425.6 kbBA00001735.39[32.88]436064..461681ICE with experimental supportGMP-synthase gene (SAV0391)Tn5801Bacteroides uniformis WH207Meng LIU (Mia), Oliver He159http://202.120.12.136/ICEberg2/feature_page.php?ice_id=15933.4 kbHemolytic StreptococciNC_00436838.11[35.63]1163887..1197331ICE with experimental supportIntergenic regions upstream of &sigma;-A promotersTnGBS2 (genomic island X)Meng LIU (Mia), Oliver He242http://202.120.12.136/ICEberg2/feature_page.php?ice_id=24271 kbAE01712533.15[35.93]223218..294244ICE with experimental supportHH0233/HH0302HHGI1Meng LIU (Mia), Oliver He152http://202.120.12.136/ICEberg2/feature_page.php?ice_id=15277.1 kbBacteroides fragilisCR62692745.44[43.19]1727162..1804281ICE with experimental supportCTn9343Meng LIU (Mia), Oliver He375http://202.120.12.136/ICEberg2/feature_page.php?ice_id=37592.5 kbAM94275944.85[38.9]2793762..2886224ICE with experimental supporttRNA-Phe (PMIt057)ICEPm1Meng LIU (Mia), Oliver He394http://202.120.12.136/ICEberg2/feature_page.php?ice_id=39451.4 kbCP00183434.99[34.91]2295682..2347036ICE with experimental supportTTATACCATAATTACTn6098Meng LIU (Mia), Oliver He396http://202.120.12.136/ICEberg2/feature_page.php?ice_id=39642.7 kbCP00121733.95[38.81]451991..494695ICE with experimental supporttype I R-M system R protein (HPP12_0436)ICEHpyP12-1Meng LIU (Mia), Oliver He436http://202.120.12.136/ICEberg2/feature_page.php?ice_id=436106 kbAJ87097454.031298..107263ICE with experimental supporttRNA-LysPPHGI-1Meng LIU (Mia), Oliver He64http://202.120.12.136/ICEberg2/feature_page.php?ice_id=64100.9 kbBacteroides spp.; Escherichia coliAY34559547.491..100903ICE with experimental supportAATCTGNNAAATCTnBSTMeng LIU (Mia), Oliver He66http://202.120.12.136/ICEberg2/feature_page.php?ice_id=66114.3 kbEscherichia coliFN29849654.9511966..126312ICE with experimental supporttRNA-PheCTnscr94Meng LIU (Mia), Oliver He67http://202.120.12.136/ICEberg2/feature_page.php?ice_id=6733.3 kbEnterococcus faeciumFN55543634.691..33262ICE with experimental supportribosomal L31 geneTn6000 (EfcTn1)Meng LIU (Mia), Oliver He71http://202.120.12.136/ICEberg2/feature_page.php?ice_id=7193.9 kbSalmonella enterica serovar Typhimurium and Yersinia pseudotuberculosisGU72539250.8477..93971ICE with experimental supporttRNA-PheICEEc2Meng LIU (Mia), Oliver He74http://202.120.12.136/ICEberg2/feature_page.php?ice_id=7454.4 kbEnterobacteriaceaeAM22967853.06292..54752ICE with experimental supporttRNA-AsnICEEcIHE3034-1Meng LIU (Mia), Oliver He77http://202.120.12.136/ICEberg2/feature_page.php?ice_id=7763.1 kbStreptococcus equiFM20488330.6[41.28]1206317..1269371ICE with experimental supportICESe2Meng LIU (Mia), Oliver He92http://202.120.12.136/ICEberg2/feature_page.php?ice_id=9233.8 kbEnterococcus faecalis; Enterococcus faecium; Clostridium symbiosumAF19232952.831..33805ICE with experimental supportTn1549Meng LIU (Mia), Oliver He102http://202.120.12.136/ICEberg2/feature_page.php?ice_id=10229.2 kbDQ32178639.9867..29238ICE with experimental supportTn5386Meng LIU (Mia), Oliver He438http://202.120.12.136/ICEberg2/feature_page.php?ice_id=438240.8 kbNC_01556366.26[66.72]1833691..2074538ICE with experimental supportDelCs14_1618phn IslandMeng LIU (Mia), Oliver He439http://202.120.12.136/ICEberg2/feature_page.php?ice_id=43965.6 kbStreptococcus pyogenes 24RFFR69105536.41659..67233ICE with experimental supportrum (23S rRNA m(5)U 1939 methyltransferase)ICESp2905Meng LIU (Mia), Oliver He440http://202.120.12.136/ICEberg2/feature_page.php?ice_id=44082.2 kbEscherichia coli HK22511; Pasteurella multocida E348-08 (capsular type F); Mannheimia haemolytica 39229CP00302241.9273284..355497ICE with experimental supporttRNA-Leu [DRs: GATTTTGAATCAA]ICEPmu1Meng LIU (Mia), Oliver He937http://202.120.12.136/ICEberg2/feature_page.php?ice_id=937131.5 kbBacteroides fragilis 638RKJ81675346.081..131471ICE with experimental supportGAAAGTGAA or TTTGACTnHybMeng LIU (Mia), Oliver He861http://202.120.12.136/ICEberg2/feature_page.php?ice_id=86128 kbClostridium difficile; Enterococcus faecalisHG47534639.061..28014ICE with experimental support7 different instertion sites in Clostridium difficile ;tRNAArg(in Enterococcus faecalis)Tn6194-likeMeng LIU (Mia), Oliver He1079http://202.120.12.136/ICEberg2/feature_page.php?ice_id=107964.4 kbLegionella pneumophila JR32CP000675392781725..2846914ICE with experimental supporttRNAMetLpcGI-2Meng LIU (Mia), Oliver He1091http://202.120.12.136/ICEberg2/feature_page.php?ice_id=109142.7 kbLegionella pneumophila JR32 Sm; Legionella micdadei (ATCC 33218)CP00067539.44614497..656813ICE with experimental supporttRNAPro (lpc2778)Trb-1Type IV coupling protein (T4CP) is a hexameric ATPase that links translocating substrates to the transenvelope secretion conduit.Meng LIU (Mia), Oliver HeT4CPhttps://www.nature.com/articles/nmicrobiol2017114type IV coupling proteinMeng LIU (Mia), Oliver He1096http://202.120.12.136/ICEberg2/feature_page.php?ice_id=1096445.2 kbNC_0149235680050..6125270ICE with experimental supportICEMcSym(1271)-alphaMeng LIU (Mia), Oliver He1101http://202.120.12.136/ICEberg2/feature_page.php?ice_id=110123 kbNC_0149232669947..2692919ICE with experimental supportICEMcSym(1271)-betaThe mating pair formation (Mpf) system functions as a secretion machinery for intercellular DNA transfer during bacterial conjugation.Meng LIU (Mia), Oliver Hehttps://www.ncbi.nlm.nih.gov/pubmed/15907535mating pair formationMPF(F) is one of four MPF familes that have been described in Proteobacteria based on plasmid F.Meng LIU (Mia), Oliver Hehttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4027160/MPF(F)MPF(T) is one of four MPF familes that have been described in Proteobacteria based on the T-DNA conjugation system of A. tumefaciens plasmid Ti.Meng LIU (Mia), Oliver Hehttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4027160/VirB-like mating pair systems (MPF(T)) are the most numerous among the four MPF classes encompassing the conjugation systems of Proteobacteria and closely related taxa.MPF(T)MPF(I) is one of four MPF familes that have been described in Proteobacteria based on the IncI plasmid R64.Meng LIU (Mia), Oliver Hehttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4027160/MPF(I)MPF(G) is one of four MPF familes that have been described in Proteobacteria based on ICEHIN1056.Meng LIU (Mia), Oliver Hehttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4027160/MPF(G)T4SS ATPase is the enzyme which energizes the T4SS system from the cytoplasm, driving the complex assembly and substrate translocation through the channel.Meng LIU (Mia), Oliver Hehttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070162/VirB4 and TraU are the major ATPases founded in ICEs.T4SS ATPaseMeng LIU (Mia), Oliver He1106http://202.120.12.136/ICEberg2/feature_page.php?ice_id=11067.8 kbNC_0149232444639..2452398ICE with experimental supportICEMcSym(1271)-gammaStreptococcus thermophilus CNRZ368T4SS are cell envelope-spanning complexes that form a channel through which DNA and proteins can travel from the cytoplasm of the donor cell to the cytoplasm of the recipient cell. T4SS is one of important secretion systems and usually consists of several components: mating-pair formation proteins (MPFs), which serve to establish physical contacts with a recipient bacterium; and, finally, a coupling protein (T4cp), which binds MOB and ssDNA to MPF .Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/SecReT4/https://en.wikipedia.org/wiki/Secretiontype IV secretion systemT4SS in Gram negative bacteriaMeng LIU (Mia), Oliver HeDue to differences in cell membrane structure, Gram-positive and Gram-negative bacteria may have different T4SS organization and features.type IV secretion system in Gram negative bacteriaT4SS in Gram positive bacteriaMeng LIU (Mia), Oliver HeDue to differences in cell membrane structure, Gram-positive and Gram-negative bacteria may have different T4SS organization and features.type IV secretion system in Gram positive bacteriaThe integration and excision module refers to those genes and sequence within the ICE responsible for the integration and excision of the element from the host chromosome, including genes encoding the integrase and or recombination directionality factor (also known as excisionase, which influences the direction of recombination mediated by the integrase to favor excision).Meng LIU (Mia), Oliver Herecombination module componenthttps://academic.oup.com/nar/article/47/D1/D660/5165266ICE integration and excision moduleOne family of recombinases based on amino acid sequence homology and mechanistic relatedness. Tyrosine is the conserved nucleophilic amino acid residue that tyrosine recombinases use to attack the DNA and which becomes covalently linked to it during strand exchange.Meng LIU (Mia), Oliver Hehttps://en.wikipedia.org/wiki/Site-specific_recombinationtyrosine recombinase is the most common integrase seen in T4SS-type ICEstyrosine recombinaseOne family of recombinases based on amino acid sequence homology and mechanistic relatedness. Serine is the conserved nucleophilic amino acid residue that serine recombinases use to attack the DNA and which becomes covalently linked to it during strand exchange.Meng LIU (Mia), Oliver Hehttps://en.wikipedia.org/wiki/Site-specific_recombinationserine recombinase is the second most common integrase seen in T4SS-type ICEsserine recombinaseA transposase enzyme with the DDE motif.Meng LIU (Mia), Oliver Hehttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2991504/DDE transposase is the third most common integrase seen in T4SS-type ICEsDDE transposaseThe oriT region, which is usually tens to hundreds of base pairs in length, contains a conserved nick region (flanking the nic site) and variable numbers of inverted repeats (IRs)Meng LIU (Mia), Oliver HeoriTorigin of transferhttp://bioinfo-mml.sjtu.edu.cn/oriTDBorigin of transfer sequenceA short DNA sequence that recombinases recognize, bind to and then cleave the DNA backbone, exchange the two DNA helices involved and rejoin the DNA strands.Meng LIU (Mia), Oliver Hehttps://en.wikipedia.org/wiki/Site-specific_recombinationrecombination attachment siteThe integration reaction is catalyzed by the integrase and, as a result of the site-specific recombination, will lead to direct repeats (typically between 10 and 60 bp) forming on either end of the integrated element, that are now named attL (left end) and attR (right end).Meng LIU (Mia), Oliver Hehttps://academic.oup.com/femsre/article/41/4/512/3089980attLThe integration reaction is catalyzed by the integrase and, as a result of the site-specific recombination, will lead to direct repeats (typically between 10 and 60 bp) forming on either end of the integrated element, that are nownamed attL (left end) and attR (right end).Meng LIU (Mia), Oliver Hehttps://academic.oup.com/femsre/article/41/4/512/3089980attRattB is the attachment site in the host chromosome during the recombination.Meng LIU (Mia), Oliver Hehttps://academic.oup.com/femsre/article/41/4/512/3089980attBMeng LIU (Mia), Oliver HeattPattI (or attP) is the attachment site on the circular ICE during the recombination.attIAfter transfer, the circular ICE integrates into a replicon, mainly at the 3' end of a tRNA or protein-encoding gene, which is called insertion siteMeng LIU (Mia), Oliver Hehttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2566197/3 end of a tRNA gene (tRNALeu, tRNAThr, or tRNALys), a gene encoding a ribosomal protein (rpsI, rplL, or rpmG-3), or the guaA gene are the common insertion site of ICE.insertion siteMeng LIU (Mia), Oliver He1098http://202.120.12.136/ICEberg2/feature_page.php?ice_id=1098528.5 kbCP0160796351798..6880279ICE with experimental supportICEMlSym(NZP2037)-alphaMeng LIU (Mia), Oliver He1103http://202.120.12.136/ICEberg2/feature_page.php?ice_id=110327.6 kbCP0160793031358..3058942ICE with experimental supportICEMlSym(NZP2037)-betaMeng LIU (Mia), Oliver He1108http://202.120.12.136/ICEberg2/feature_page.php?ice_id=11086.2 kbCP0160792577929..2584131ICE with experimental supportICEMlSym(NZP2037)-gammaMeng LIU (Mia), Oliver He811http://202.120.12.136/ICEberg2/feature_page.php?ice_id=81194.2 kbHE96302943.961..94189ICE with experimental supporttRNA (uracil-5)-methyltransferase rumA; CACGTGGAGTGCGTAGTGTT(attL); TTCTCAAGGACCAGACAACA(attR)ICESluvanMeng LIU (Mia), Oliver He812http://202.120.12.136/ICEberg2/feature_page.php?ice_id=81249.2 kbStreptococcus pyogenesHE80267735.241..49160ICE with experimental supportrpmHICESp1116Meng LIU (Mia), Oliver He743http://202.120.12.136/ICEberg2/feature_page.php?ice_id=74329.7 kbStreptococcus salivarius; Streptococcus thermophilus; Enterococcus faecalisLT62282735.331..29716ICE with experimental supportfdaICE_SsaF1-4_fdaMeng LIU (Mia), Oliver He745http://202.120.12.136/ICEberg2/feature_page.php?ice_id=74530.2 kbStreptococcus salivarius; Streptococcus thermophilus; Enterococcus faecalisLT62282935.611..30222ICE with experimental supportfdaICE_SsaF4-2_fdaMeng LIU (Mia), Oliver He829http://202.120.12.136/ICEberg2/feature_page.php?ice_id=82988.9 kbStreptococcus suis P1/7RF; Streptococcus suis SS-1RFKX07788836.81875..89748ICE with experimental supportrplLICESsu05SC260Meng LIU (Mia), Oliver He837http://202.120.12.136/ICEberg2/feature_page.php?ice_id=83729.7 kbKU21570434.141..29661ICE with experimental supportICESsuNC28Streptococcus thermophilus CNRZ385Haemophilus influenzae 1056Ralstonia oxalatica A5Streptococcus parauberis NUF1049Streptococcus pneumoniae 05P294Streptococcus pneumoniae DP1322Recombination directionality factors (RDFs) are a diverse group of proteins involved in controlling the directionality of integrase-mediated site-specific recombination reactions.Meng LIU (Mia), Oliver HeRDFhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC55702/Typically, RDFs are small DNA-binding proteins acting as accessory factors to influence the choice of substrates that are recombined by their cognate recombinaseXisrecombination directionality factorStreptococcus pneumoniae Ar4Streptococcus oralis F.MI.5The regulation module refers to those genes and sequence contributing to stabilization and maintenance of ICEs.Meng LIU (Mia), Oliver Hehttps://academic.oup.com/nar/article/47/D1/D660/5165266ICE regulation moduletoxin–antitoxin system is small genetic element composed of a stable toxin protein and a labile cognate antitoxin encoded by a bicistronic locus. TA system is involved in regulation of bacterial metabolic activity and plays important role in plasmid maintenance and ICE post-segregational killing systems.Meng LIU (Mia), Oliver Hehttp://bioinfo-mml.sjtu.edu.cn/TADB2/https://academic.oup.com/femspd/article/70/3/240/567411Toxin-antitoxin (TA) loci play a role in bacterial stress physiology and the stabilisation of horizontally acquired elements. TA loci are found abundantly distributed among free-living Bacteria and Archaea.toxin–antitoxin systemtrueRestriction-modification system is a defense system developed by bacteria to defend themselves from invasions of phage (or viruses ). Restriction-modification system composed of a restriction endonuclease enzyme and a methylase enzyme and each bacterial species and strain has their own combination of restriction and methylating enzymes.Meng LIU (Mia), Oliver Hehttps://www.ndsu.edu/pubweb/~mcclean/plsc731/dna/dna5.htmDNA restriction-modification systemtrueListeria monocytogenes TTH-2007Listeria monocytogenes strain TTH-2007the integration and excision module of ICE BTF-37.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/BTF-37 IEMStaphylococcus rostri RST11Photobacterium damselae subsp. piscicida PC554.2Proteus mirabilis 08MAS1586Proteus mirabilis TJ1809A role played by a material entity where the circular ICE integrates into a replicon after transfer.Meng LIU (Mia), Oliver Heinsertion site roleProteus mirabilis JN7Proteus mirabilis 09MAS2407the integration and excision module of ICE CTn341.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/CTn341 IEMthe integration and excision module of ICE CTnDOT.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/CTnDOT IEMthe integration and excision module of ICE CTnERL.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/CTnERL IEMthe integration and excision module of ICE ICEVchAng1.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchAng1 IEMMeng LIU (Mia), Oliver He1035http://202.120.12.136/ICEberg2/feature_page.php?ice_id=103594.3 kbKX24340346.771..94340ICE with experimental supportICEPvuCHN2213Meng LIU (Mia), Oliver He1068http://202.120.12.136/ICEberg2/feature_page.php?ice_id=106897.4 kbKC88625746.79528..97877ICE with experimental supportICEVchNep1Meng LIU (Mia), Oliver He1069http://202.120.12.136/ICEberg2/feature_page.php?ice_id=106997 kbKC88625846.79528..97570ICE with experimental supportICEVchNig1The Tn<em>916</em> family was defined by <a href="http://www.ncbi.nlm.nih.gov/pubmed/19464182">Roberts et al (2009)</a>. Elements belonging to the Tn916 family are defined by the following criteria: they must have the general organization shown in the following figure based on the figure from Roberts et al, and they must have a core region (conjugation and regulation module) that is similar in sequence and structure to the original Tn<em>916</em> at the DNA level. Exceptions are some conjugative transposons, such as Tn<em>1549</em> which have been previously classified in this family and those with a high degree of protein similarity as described in corresponding references. <br /> <img src="images/Tn916.PNG" width="620" height="183" border="0" align="middle" />Meng LIU (Mia), Oliver HeICEberg databasehttp://db-mml.sjtu.edu.cn/ICEberg/Tn916 family ICEMeng LIU (Mia), Oliver He103http://202.120.12.136/ICEberg2/feature_page.php?ice_id=10320.7 kbBacillus subtilis; Clostridium difficileAM18035538.32[29.06]585384..606040ICE with experimental supportAT rich regionsTn5397Meng LIU (Mia), Oliver He303http://202.120.12.136/ICEberg2/feature_page.php?ice_id=30318 kbU4993938.75[38.53]1344..19375ICE with experimental supportAT rich regionsTn916(pAM120)Meng LIU (Mia), Oliver He306http://202.120.12.136/ICEberg2/feature_page.php?ice_id=30618 kbAY85584138.73[36.1]40068..58099ICE with experimental supportAT rich regionsthis ICE was found in Enterococcus faecalis plasmid pCF10Tn925Meng LIU (Mia), Oliver He307http://202.120.12.136/ICEberg2/feature_page.php?ice_id=30718 kbFN55010238.71..18032ICE with experimental supportAT rich regionsTn916(RST11)Meng LIU (Mia), Oliver He308http://202.120.12.136/ICEberg2/feature_page.php?ice_id=30818 kbAB46815938.713016..21046ICE with experimental supportAT rich regionsICESpaNUF1049Meng LIU (Mia), Oliver He318http://202.120.12.136/ICEberg2/feature_page.php?ice_id=31820.8 kb38.46ICE with experimental supportAT rich regionsTn6085bMeng LIU (Mia), Oliver He319http://202.120.12.136/ICEberg2/feature_page.php?ice_id=31920.8 kbHM24362138.466653..27441ICE with experimental supportAT rich regionsTn6085aMeng LIU (Mia), Oliver He328http://202.120.12.136/ICEberg2/feature_page.php?ice_id=32822.3 kbHM24362238.4234197..56508ICE with experimental supportAT rich regionsTn6084Meng LIU (Mia), Oliver He321http://202.120.12.136/ICEberg2/feature_page.php?ice_id=32125.1 kbAM41004437.981..25101ICE with experimental supportAT rich regionsTn6003Meng LIU (Mia), Oliver He325http://202.120.12.136/ICEberg2/feature_page.php?ice_id=32526.4 kbAB42662037.891..26390ICE with experimental supportAT rich regionsTn2010the integration and excision module of ICE ICEVchAng2.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchAng2 IEMthe integration and excision module of ICE ICEVchAng3.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchAng3 IEMthe integration and excision module of ICE ICEVchBan1.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchBan1 IEMthe integration and excision module of ICE ICEVchBan2.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchBan2 IEMthe integration and excision module of ICE ICEVchBan3.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchBan3 IEMthe integration and excision module of ICE ICEVchBan4.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchBan4 IEMthe integration and excision module of ICE ICEVchBan5.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchBan5 IEMthe integration and excision module of ICE ICEVchBan6.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchBan6 IEMa role played by a material entity that often involves in the conjugal process.Meng LIU (Mia), Oliver Heconjugation module component rolea role played by a protein which links translocating substrates to the transenvelope secretion conduit.Meng LIU (Mia), Oliver HeT4CP roletype IV coupling protein roleProteus mirabilis TJ3335Proteus mirabilis JN14a role played by a protein that energizes the T4SS system from the cytoplasm and drives the complex assembly and substrate translocation through the channel.Meng LIU (Mia), Oliver HeT4SS ATPase roleAmycolatopsis mediterranei LBG A3136Proteus vulgaris 08MAS2213A role played by a gene that encodes a protein which is part of T4SS (a cell envelope-spanning complexes that form a channel through which DNA and proteins can travel from the cytoplasm of the donor cell to the cytoplasm of the recipient cell. )Meng LIU (Mia), Oliver HeT4SS gene component roletype IV secretion system gene component roleShewanella putrefaciens W3-18-1Bacteroides fragilis 86-5443-2-2Clostridium difficile CII7Clostridium difficile strain CII7A role played by a protein that mediates an exchange reaction between two DNA templates and results in integration of DNA from one of the templates into the other.Meng LIU (Mia), Oliver Heintegrase roleA role played by a material entity that contains a conserved nick region (flanking the nic site) and variable numbers of inverted repeats (IRs) and served as origin site of transfer.Meng LIU (Mia), Oliver HeoriT roleorigin of transfer roleA role played by a short DNA sequence that recombinases recognize, bind to and then cleave the DNA backbone, exchange the two DNA helices involved and rejoin the DNA strands.Meng LIU (Mia), Oliver Herecombination attachment site roleMeng LIU (Mia), Oliver Heprotein of Escherichia coli ECOR31Enterococcus casseliflavus 664.1H1Enterococcus faecalis BM4382Enterococcus faecium D344REscherichia coli BEN374Salmonella bongori CEIM46082the integration and excision module of ICE ICEVchBan7.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchBan7 IEMSalmonella enterica subsp. enterica serovar Senftenberg, strain 5494-57Salmonella enterica subsp. enterica serovar Senftenberg, 5494-57Staphylococcus aureus JCSC6826Staphylococcus aureus HDG2Streptococcus agalactiae Sag37Streptococcus dysgalactiae subsp. equisimilis NS3396Streptococcus lutetiensis 5-F9Streptococcus pneumoniae Pn19Streptococcus pyogenes C1Streptococcus pyogenes iB21Streptococcus pyogenes MB56Spyo009A role played by a protein that controlls the directionality of integrase-mediated site-specific recombination reactions.Meng LIU (Mia), Oliver HeRDF rolerecombination directionality factor rolea role played by a material entity that involves in stabilization and maintenance of ICEs.Meng LIU (Mia), Oliver Heregulation module component rolea role played by a material entity that often exists inside ICEs as the cargo genes and can confer the hosts with selective advantages.Meng LIU (Mia), Oliver Heaccessory module component rolea role played by a material entity that can confer the the ability of bacteria and other microorganisms to resist the effects of an antibiotic to which they were once sensitive.Meng LIU (Mia), Oliver Heantibiotic resistance gene roleA role played by a gene that encodes products which assist the bacterium colonize the host at the cellular level and are either secretory, membrane associated or cytosolic in nature.Meng LIU (Mia), Oliver HeVF gene rolevirulence factor gene rolethe integration and excision module of ICE ICEVchBan9.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchBan9 IEMthe integration and excision module of ICE ICEVchInd1.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchInd1 IEMthe integration and excision module of ICE ICEVchInd2.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchInd2 IEMStreptococcus pyogenes strain A-3Streptococcus pyogenes 2812Athe integration and excision module of ICE ICEVchInd3.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchInd3 IEMthe integration and excision module of ICE ICEVchInd4.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchInd4 IEMStreptococcus salivarius strain F1-4Streptococcus salivarius strain F4-2gene of Escherichia coli ECOR31protein-coding gene of Escherichia coli ECOR31RNA gene of Escherichia coli ECOR31A role played by a protein that nicks the dsDNA and remains covalently bound to the resulting ssDNAMeng LIU (Mia), Oliver Herelaxase rolea ICE of GammaproteobacteriaMeng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICE in GammaproteobacteriaMeng LIU (Mia), Oliver He326http://202.120.12.136/ICEberg2/feature_page.php?ice_id=32621.2 kbHQ66384938.231..21169ICE with experimental supportAT rich regionsTn6087Meng LIU (Mia), Oliver He47http://202.120.12.136/ICEberg2/feature_page.php?ice_id=4718 kbStreptococcus pneumoniae; Streptococcus gordonii; Streptococcus pyogenes; Streptococcus agalactiae;Enterococcus faecalis; Bacillus subtilisFJ71116038.851..18033ICE with experimental supportAT rich regionsTn5251 (part of Tn5253)Meng LIU (Mia), Oliver He45http://202.120.12.136/ICEberg2/feature_page.php?ice_id=4518 kbEnterococcus faecalis; Butyrivibrio proteoclasticus; Streptococcus spp.; Lactococcus lactis; Lactobacillus paracasei; Neisseria sp.; Escherichia coli; Desulfitobacterium dehalogenans; Bacillus subtilis; Bacillus thuringiensis subsp. IsraelensisU0942238.751..18032ICE with experimental supportAT rich regionsTn916Meng LIU (Mia), Oliver He62http://202.120.12.136/ICEberg2/feature_page.php?ice_id=6220.9 kbStreptococcus cristatus; Streptococcus sanguinisAY89875038.231..20880ICE with experimental supportCTn6002Meng LIU (Mia), Oliver He862http://202.120.12.136/ICEberg2/feature_page.php?ice_id=86221.3 kbJX12010237.931..21322ICE with experimental supportTn6198Streptococcus suis 32457Streptococcus suis 05SC260Streptococcus suis strain nc286A7Yersinia pseudotuberculosis 32777ICEKp1 CMMeng LIU (Mia), Oliver HeT4ASS type T4SS geneMeng LIU (Mia), Oliver Hetype F T4SS geneMeng LIU (Mia), Oliver Hetype I T4SS geneMeng LIU (Mia), Oliver Hetype P T4SS geneMeng LIU (Mia), Oliver HeT4BSS type T4SS genethe integration and excision module of ICE ICEVchInd5 [ICEVchHai1].Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchInd5 [ICEVchHai1] IEMthe integration and excision module of ICE ICEVchMex1.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchMex1 IEMthe integration and excision module of ICE ICEVchMoz2.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchMoz2 IEMthe integration and excision module of ICE ICEVchMoz3.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchMoz3 IEMthe integration and excision module of ICE ICEVchMoz4.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchMoz4 IEMthe integration and excision module of ICE ICEVchMoz5.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchMoz5 IEMthe integration and excision module of ICE ICEVchMoz6.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchMoz6 IEMthe integration and excision module of ICE ICEVchMoz7.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchMoz7 IEMthe integration and excision module of ICE ICEVchMoz8.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchMoz8 IEMthe integration and excision module of ICE ICEVchMoz9.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchMoz9 IEMthe integration and excision module of ICE ICEVchSL1.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchSL1 IEMthe integration and excision module of ICE ICEVchVie1.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVchVie1 IEMthe integration and excision module of ICE ICEVflInd1.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEVflInd1 IEMthe integration and excision module of ICE ICEPalBan1.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEPalBan1 IEMthe integration and excision module of ICE ICEPdaSpa1.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEPdaSpa1 IEMthe integration and excision module of ICE ICESpuPO1.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICESpuPO1 IEMthe integration and excision module of ICE ICEPmiUSA1.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEPmiUSA1 IEMthe integration and excision module of ICE ICEPmiJpn1.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEPmiJpn1 IEMthe integration and excision module of ICE pMERPH.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/pMERPH IEMthe integration and excision module of ICE R391.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/R391 IEMthe integration and excision module of ICE SXT(MO10).Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/SXT(MO10) IEMthe integration and excision module of ICE Tn916.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/Tn916 IEMthe integration and excision module of ICE Tn4371.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/Tn4371 IEMthe integration and excision module of ICE Tn5251 (part of Tn5253).Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/Tn5251 (part of Tn5253) IEMthe integration and excision module of ICE ICEclc(B13).Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEclc(B13) IEMthe integration and excision module of ICE ICEclc(JS705).Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEclc(JS705) IEMthe integration and excision module of ICE ICEBs1.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEBs1 IEMthe integration and excision module of ICE ICEHin1056.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEHin1056 IEMthe integration and excision module of ICE CTn6002.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/CTn6002 IEMthe integration and excision module of ICE CTn86.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/CTn86 IEMthe integration and excision module of ICE CTnBST.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/CTnBST IEMthe integration and excision module of ICE CTnGERM1.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/CTnGERM1 IEMthe integration and excision module of ICE CTnscr94.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/CTnscr94 IEMthe integration and excision module of ICE Tn6000 (EfcTn1).Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/Tn6000 (EfcTn1) IEMthe integration and excision module of ICE ICE6013.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICE6013 IEMthe integration and excision module of ICE ICEA(5632)-I.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEA(5632)-I IEMthe integration and excision module of ICE ICEEc1.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEEc1 IEMthe integration and excision module of ICE ICEEc2.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEEc2 IEMthe integration and excision module of ICE ICEF-I.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEF-I IEMthe integration and excision module of ICE ICEF-II.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEF-II IEMthe integration and excision module of ICE ICEEcIHE3034-1.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEEcIHE3034-1 IEMthe integration and excision module of ICE ICEMlSym(R7A).Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICEMlSym(R7A) IEMthe integration and excision module of ICE ICESde3396.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICESde3396 IEMthe integration and excision module of ICE ICESe2.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICESe2 IEMthe integration and excision module of ICE ICESt1.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICESt1 IEMthe integration and excision module of ICE ICESt3.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICESt3 IEMthe integration and excision module of ICE SXT(ET).Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/SXT(ET) IEMthe integration and excision module of ICE Tn1545.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/Tn1545 IEMthe integration and excision module of ICE Tn1549.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/Tn1549 IEMthe integration and excision module of ICE Tcr Emr 7853.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/Tcr Emr 7853 IEMthe integration and excision module of ICE Tn5030.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/Tn5030 IEMthe integration and excision module of ICE Tn5252 (part of Tn5253).Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/Tn5252 (part of Tn5253) IEMthe integration and excision module of ICE Tn5276.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/Tn5276 IEMthe integration and excision module of ICE Tn5281.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/Tn5281 IEMthe integration and excision module of ICE Tn5307.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/Tn5307 IEMthe integration and excision module of ICE Tn5381.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/Tn5381 IEMthe integration and excision module of ICE Tn5383.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/Tn5383 IEMthe integration and excision module of ICE Tn5385.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/Tn5385 IEMthe integration and excision module of ICE Tn5386.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/Tn5386 IEMthe integration and excision module of ICE Tn5397.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/Tn5397 IEMthe integration and excision module of ICE Tn6009.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/Tn6009 IEMthe integration and excision module of ICE Tn916S.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/Tn916S IEMMeng LIU (Mia), Oliver HeBAH64175.1(Int)BAH64176.1(YbtS)BAH64177.1(YbtX)BAH64178.1(YbtQ)BAH64179.1(YbtP)BAH64180.1(YbtA)BAH64181.1(Irp2)BAH64182.1(Irp1)BAH64183.1(YbtU)BAH64184.1(YbtT)yersiniabactin siderophore biosynthetic proteinBAH64185.1(YbtE)BAH64186.1(FyuA)BAH64187.1BAH64188.1(AlpA2)BAH64189.1BAH64190.1BAH64191.1BAH64192.1BAH64193.1BAH64194.1BAH64195.1BAH64196.1(VagC)BAH64197.1(VagD)BAH64198.1BAH64199.1(IroN)BAH64200.1(IroB)BAH64201.1(IroC)BAH64202.1(IroD)BAH64203.1(PagO)BAH64204.1BAH64205.1BAH64206.1(RmpA)BAH64207.1BAH64208.1BAH64209.1BAH64210.1BAH64211.1BAH64212.1(VirB1)BAH64213.1(VirB2)BAH64214.1(VirB3-4)BAH64215.1(VirB5)BAH64216.1BAH64217.1(VirB6)BAH64218.1(VirB8)BAH64219.1(VirB9)BAH64220.1(VirB10)BAH64221.1(VirB11)BAH64222.1BAH64223.1BAH64224.1BAH64225.1BAH64226.1(MobB)BAH64227.1(MobC)BAH64228.1(ArdC)BAH64229.1BAH64230.1BAH64231.1BAH64232.1BAH64233.1BAH64234.1BAH64235.1BAH64236.1Bacteroides fragilis LV23Bacteroides thetaiotaomicron 7853Butyrivibrio fibrisolvens 1.230Clostridium perfringens CW459Elizabethkingia anophelis CSID_3015183678Enterococcus faecalis JH2-7Enterococcus faecium 9830414-1Klebsiella pneumoniae 41Lactococcus lactis 11454Lactococcus lactis FI5876Lactococcus lactis R5Lactococcus lactis subsp. lactis ML3Micromonospora rosaria SCC2095Pectobacterium carotovorum subsp. brasiliensis ICMPProteus mirabilis TUM4660Pseudomonas putida KF715Saccharopolyspora endophytica YIM 61095Staphylococcus aureus 1591Staphylococcus aureus 21995Staphylococcus aureus 22034Staphylococcus aureus 34801Staphylococcus aureus 35366Staphylococcus aureus 35414Staphylococcus aureus 35679Staphylococcus aureus 4520Staphylococcus aureus 4865Staphylococcus aureus 5331Staphylococcus aureus 5377Staphylococcus aureus 617Staphylococcus aureus 7215190-1Staphylococcus aureus 7215311-1Staphylococcus aureus 7312330-1Staphylococcus aureus 7412791-1Staphylococcus aureus 7413093-4Staphylococcus aureus 7413714-1Staphylococcus aureus 7512166-1Staphylococcus aureus 7512986-1Staphylococcus aureus 7611280-5Staphylococcus aureus 7612628-4Staphylococcus aureus 7711730-1Staphylococcus aureus 8797Staphylococcus aureus 9877324-3_H39Staphylococcus aureus SW356Staphylococcus aureus USA42Streptococcus agalactiae Sag236Streptococcus agalactiae SagTR7Streptococcus dysgalactiae subsp. equisimilis (Sde5580)Streptococcus intermedius 15.3T.2Streptococcus pneumoniae BM4200Streptococcus pneumoniae BM6001Streptococcus pneumoniae J93/183Streptococcus pneumoniae J93/292Streptococcus pneumoniae KD6Streptococcus pneumoniae N24Streptococcus pneumoniae PN02/2531Streptococcus pneumoniae SP1000Streptococcus pneumoniae SpnA213Streptococcus pneumoniae SpnF21Streptococcus pyogenes 12SN-TcStreptococcus pyogenes C-105Streptococcus pyogenes Spy005Streptococcus sanguinis FC1Streptococcus suis HB1011Streptomyces ambofaciens ATCC 15154 B3Streptomyces cyaneus ATCC 14921Streptomyces glaucescens GLA000Vibrio alginolyticus V86Vibrio cholerae 00LA1Vibrio cholerae 15AMOZVibrio cholerae 16AMOZVibrio cholerae 204Vibrio cholerae 3AMOZVibrio cholerae 5556Vibrio cholerae 5594Vibrio cholerae 7698Vibrio cholerae 8AMOZVibrio cholerae Chn108Vibrio cholerae HKO139-SXTVibrio cholerae MCV09Vibrio cholerae Non-O1 698Vibrio cholerae Non-O1 7AMOZVibrio cholerae O1 175Vibrio cholerae O1 582Vibrio cholerae O1 90Vibrio cholerae O1 AC1923Vibrio cholerae O1 AC1924Vibrio cholerae O1 BI142Vibrio cholerae O1 biovar El Tor 1999Vibrio cholerae V21Vibrio fluvialis H-08942Vibrio parahaemolyticus Chn25Vibrio scophthalmi ACC7Vibrio scophthalmi NC1Vibrio scophthalmi YF7Vibrio splendidus V69Meng LIU (Mia), Oliver He458http://202.120.12.136/ICEberg2/feature_page.php?ice_id=458Escherichia coli CAG18420; Escherichia coli BI533ICE with experimental supportprfCICEEniSpa1Meng LIU (Mia), Oliver He459http://202.120.12.136/ICEberg2/feature_page.php?ice_id=459Escherichia coli CAG18420; Escherichia coli BI533ICE with experimental supportprfCICEEniSpa2Meng LIU (Mia), Oliver He41http://202.120.12.136/ICEberg2/feature_page.php?ice_id=41Escherichia coli; Klebsiella pneumoniae; Salmonella enterica serovar Typhimurium; Citrobacter koseriICE with experimental supportprfCICEPmiJpn1Meng LIU (Mia), Oliver He109http://202.120.12.136/ICEberg2/feature_page.php?ice_id=109~85 kbICE with experimental supportprfCR997Meng LIU (Mia), Oliver He144http://202.120.12.136/ICEberg2/feature_page.php?ice_id=144Proteus hauseriICE with experimental supportprfCR705Meng LIU (Mia), Oliver He145http://202.120.12.136/ICEberg2/feature_page.php?ice_id=145Proteus hauseriICE with experimental supportprfCR706Meng LIU (Mia), Oliver He142http://202.120.12.136/ICEberg2/feature_page.php?ice_id=142ICE with experimental supportprfCR392Meng LIU (Mia), Oliver He143http://202.120.12.136/ICEberg2/feature_page.php?ice_id=143ICE with experimental supportprfCR397Meng LIU (Mia), Oliver He146http://202.120.12.136/ICEberg2/feature_page.php?ice_id=146ICE with experimental supportprfCR748Meng LIU (Mia), Oliver He147http://202.120.12.136/ICEberg2/feature_page.php?ice_id=147ICE with experimental supportprfCR749Meng LIU (Mia), Oliver He1034http://202.120.12.136/ICEberg2/feature_page.php?ice_id=1034ICE with experimental supportICEPspSpa1Meng LIU (Mia), Oliver He461http://202.120.12.136/ICEberg2/feature_page.php?ice_id=461Escherichia coli CAG18420; Escherichia coli BI533ICE with experimental supportprfCICEShaPor1Meng LIU (Mia), Oliver He42http://202.120.12.136/ICEberg2/feature_page.php?ice_id=42ICE with experimental supportprfCpMERPHMeng LIU (Mia), Oliver He1036http://202.120.12.136/ICEberg2/feature_page.php?ice_id=1036110.3 kb[46.3]ICE with experimental supportICESh95Meng LIU (Mia), Oliver He460http://202.120.12.136/ICEberg2/feature_page.php?ice_id=460Escherichia coli CAG18420; Escherichia coli BI533ICE with experimental supportprfCICEValPor1Meng LIU (Mia), Oliver He447http://202.120.12.136/ICEberg2/feature_page.php?ice_id=447ICE with experimental supportprfCICEValSpa1Meng LIU (Mia), Oliver He136http://202.120.12.136/ICEberg2/feature_page.php?ice_id=136ICE with experimental supportprfCICEVchLao1Meng LIU (Mia), Oliver He28http://202.120.12.136/ICEberg2/feature_page.php?ice_id=28ICE with experimental supportprfCICEVchMoz5Meng LIU (Mia), Oliver He29http://202.120.12.136/ICEberg2/feature_page.php?ice_id=29ICE with experimental supportprfCICEVchMoz6Meng LIU (Mia), Oliver He108http://202.120.12.136/ICEberg2/feature_page.php?ice_id=108Escherichia coliICE with experimental supportprfCpJY1Meng LIU (Mia), Oliver He25http://202.120.12.136/ICEberg2/feature_page.php?ice_id=25ICE with experimental supportprfCICEVchMoz2Meng LIU (Mia), Oliver He31http://202.120.12.136/ICEberg2/feature_page.php?ice_id=31ICE with experimental supportprfCICEVchMoz8Meng LIU (Mia), Oliver He30http://202.120.12.136/ICEberg2/feature_page.php?ice_id=30ICE with experimental supportprfCICEVchMoz7Meng LIU (Mia), Oliver He32http://202.120.12.136/ICEberg2/feature_page.php?ice_id=32ICE with experimental supportprfCICEVchMoz9Meng LIU (Mia), Oliver He27http://202.120.12.136/ICEberg2/feature_page.php?ice_id=27ICE with experimental supportprfCICEVchMoz4Meng LIU (Mia), Oliver He1062http://202.120.12.136/ICEberg2/feature_page.php?ice_id=1062Escherichia coli MG1655ICE with experimental supportprfCICEVchChn6Meng LIU (Mia), Oliver He135http://202.120.12.136/ICEberg2/feature_page.php?ice_id=135ICE with experimental supportprfCICEVchHKo1Meng LIU (Mia), Oliver He274http://202.120.12.136/ICEberg2/feature_page.php?ice_id=274ICE with experimental supportprfCSXT(MCV09)Meng LIU (Mia), Oliver He6http://202.120.12.136/ICEberg2/feature_page.php?ice_id=6ICE with experimental supportprfCICEVchAng2Meng LIU (Mia), Oliver He26http://202.120.12.136/ICEberg2/feature_page.php?ice_id=26ICE with experimental supportprfCICEVchMoz3Meng LIU (Mia), Oliver He7http://202.120.12.136/ICEberg2/feature_page.php?ice_id=7ICE with experimental supportprfCICEVchAng3Meng LIU (Mia), Oliver He5http://202.120.12.136/ICEberg2/feature_page.php?ice_id=5ICE with experimental supportprfCICEVchAng1Meng LIU (Mia), Oliver He139http://202.120.12.136/ICEberg2/feature_page.php?ice_id=139ICE with experimental supportprfCICEVchVie0Meng LIU (Mia), Oliver He9http://202.120.12.136/ICEberg2/feature_page.php?ice_id=9ICE with experimental supportprfCICEVchBan2Meng LIU (Mia), Oliver He10http://202.120.12.136/ICEberg2/feature_page.php?ice_id=10ICE with experimental supportprfCICEVchBan3Meng LIU (Mia), Oliver He18http://202.120.12.136/ICEberg2/feature_page.php?ice_id=18ICE with experimental supportprfCICEVchInd1Meng LIU (Mia), Oliver He89http://202.120.12.136/ICEberg2/feature_page.php?ice_id=89ICE with experimental supportprfCSXT(ET)Meng LIU (Mia), Oliver He8http://202.120.12.136/ICEberg2/feature_page.php?ice_id=8ICE with experimental supportprfCICEVchBan1Meng LIU (Mia), Oliver He11http://202.120.12.136/ICEberg2/feature_page.php?ice_id=11ICE with experimental supportprfCICEVchBan4Meng LIU (Mia), Oliver He13http://202.120.12.136/ICEberg2/feature_page.php?ice_id=13ICE with experimental supportprfCICEVchBan6Meng LIU (Mia), Oliver He19http://202.120.12.136/ICEberg2/feature_page.php?ice_id=19ICE with experimental supportprfCICEVchInd2Meng LIU (Mia), Oliver He20http://202.120.12.136/ICEberg2/feature_page.php?ice_id=20ICE with experimental supportprfCICEVchInd3Meng LIU (Mia), Oliver He137http://202.120.12.136/ICEberg2/feature_page.php?ice_id=137ICE with experimental supportprfCICEVchSaf1Meng LIU (Mia), Oliver He14http://202.120.12.136/ICEberg2/feature_page.php?ice_id=14ICE with experimental supportprfCICEVchBan7Meng LIU (Mia), Oliver He34http://202.120.12.136/ICEberg2/feature_page.php?ice_id=34ICE with experimental supportprfCICEVchSL1Meng LIU (Mia), Oliver He35http://202.120.12.136/ICEberg2/feature_page.php?ice_id=35ICE with experimental supportprfCICEVchVie1Meng LIU (Mia), Oliver He149http://202.120.12.136/ICEberg2/feature_page.php?ice_id=149Escherichia coliICE with experimental supportprfCICEVflH-08942Meng LIU (Mia), Oliver He1072http://202.120.12.136/ICEberg2/feature_page.php?ice_id=1072Escherichia coli MG1655ICE with experimental supportICEVpaChn1Meng LIU (Mia), Oliver He141http://202.120.12.136/ICEberg2/feature_page.php?ice_id=141ICE with experimental supportprfCICEVpaAng1Meng LIU (Mia), Oliver He450http://202.120.12.136/ICEberg2/feature_page.php?ice_id=450Escherichia coli CAG18420; Escherichia coli BI533ICE with experimental supportprfCICEVscSpa1Meng LIU (Mia), Oliver He451http://202.120.12.136/ICEberg2/feature_page.php?ice_id=451Escherichia coli CAG18420; Escherichia coli BI533ICE with experimental supportprfCICEVscSpa2Meng LIU (Mia), Oliver He452http://202.120.12.136/ICEberg2/feature_page.php?ice_id=452Escherichia coli CAG18420; Escherichia coli BI533ICE with experimental supportprfCICEVscSpa3Meng LIU (Mia), Oliver He453http://202.120.12.136/ICEberg2/feature_page.php?ice_id=453Escherichia coli CAG18420; Escherichia coli BI533ICE with experimental supportprfCICEVspPor1Meng LIU (Mia), Oliver He454http://202.120.12.136/ICEberg2/feature_page.php?ice_id=454Escherichia coli CAG18420; Escherichia coli BI533ICE with experimental supportprfCICEVspPor2Meng LIU (Mia), Oliver He455http://202.120.12.136/ICEberg2/feature_page.php?ice_id=455Escherichia coli CAG18420; Escherichia coli BI533ICE with experimental supportprfCICEVspSpa1Meng LIU (Mia), Oliver He456http://202.120.12.136/ICEberg2/feature_page.php?ice_id=456Escherichia coli CAG18420; Escherichia coli BI533ICE with experimental supportprfCICEVspSpa2Meng LIU (Mia), Oliver He457http://202.120.12.136/ICEberg2/feature_page.php?ice_id=457Escherichia coli CAG18420; Escherichia coli BI533ICE with experimental supportprfCICEVspSpa3Meng LIU (Mia), Oliver He446http://202.120.12.136/ICEberg2/feature_page.php?ice_id=446Escherichia coli CAG18420; Photobacterium damselae subsp. damselae; Edwardsiella tarda; Shewanella putrefaciens; Vibrio anguillarumICE with experimental supportprfCICEVspPor3Vibrio splendidus ZD4Vibrio splendidus ZD5Vibrio splendidus ZF2Vibrio splendidus EB5Vibrio splendidus 14-3Meng LIU (Mia), Oliver He125http://202.120.12.136/ICEberg2/feature_page.php?ice_id=125ICE with experimental supportgene encoding a GMP-synthaseCW459tet(M)Meng LIU (Mia), Oliver He383http://202.120.12.136/ICEberg2/feature_page.php?ice_id=383ICE with experimental supportICEEfa9830414Meng LIU (Mia), Oliver He243http://202.120.12.136/ICEberg2/feature_page.php?ice_id=243ICE with experimental supportAT rich regionsthis ICE was found in Lactococcus lactis subsp. lactis plasmid pAA211ICELlapAA211Meng LIU (Mia), Oliver He244http://202.120.12.136/ICEberg2/feature_page.php?ice_id=244ICE with experimental supportAT rich regionsthis ICE was found in Lactococcus lactis subsp. lactis plasmid pAA291ICELlapAA291Meng LIU (Mia), Oliver He261http://202.120.12.136/ICEberg2/feature_page.php?ice_id=261ICE with experimental supportAT rich regionsICESau1591Meng LIU (Mia), Oliver He246http://202.120.12.136/ICEberg2/feature_page.php?ice_id=246ICE with experimental supportAT rich regionsICESau21995Meng LIU (Mia), Oliver He269http://202.120.12.136/ICEberg2/feature_page.php?ice_id=269ICE with experimental supportAT rich regionsICESau22034Meng LIU (Mia), Oliver He263http://202.120.12.136/ICEberg2/feature_page.php?ice_id=263ICE with experimental supportAT rich regionsICESau34801Meng LIU (Mia), Oliver He247http://202.120.12.136/ICEberg2/feature_page.php?ice_id=247ICE with experimental supportAT rich regionsICESau35366Meng LIU (Mia), Oliver He260http://202.120.12.136/ICEberg2/feature_page.php?ice_id=260ICE with experimental supportAT rich regionsICESau35414Meng LIU (Mia), Oliver He252http://202.120.12.136/ICEberg2/feature_page.php?ice_id=252ICE with experimental supportAT rich regionsICESau35679Meng LIU (Mia), Oliver He272http://202.120.12.136/ICEberg2/feature_page.php?ice_id=272ICE with experimental supportAT rich regionsICESau4520Meng LIU (Mia), Oliver He271http://202.120.12.136/ICEberg2/feature_page.php?ice_id=271ICE with experimental supportAT rich regionsICESau4865Meng LIU (Mia), Oliver He270http://202.120.12.136/ICEberg2/feature_page.php?ice_id=270ICE with experimental supportAT rich regionsICESau5331Meng LIU (Mia), Oliver He265http://202.120.12.136/ICEberg2/feature_page.php?ice_id=265ICE with experimental supportAT rich regionsICESau5377Meng LIU (Mia), Oliver He264http://202.120.12.136/ICEberg2/feature_page.php?ice_id=264ICE with experimental supportAT rich regionsICESau617Meng LIU (Mia), Oliver He268http://202.120.12.136/ICEberg2/feature_page.php?ice_id=268ICE with experimental supportAT rich regionsICESau7215190Meng LIU (Mia), Oliver He254http://202.120.12.136/ICEberg2/feature_page.php?ice_id=254ICE with experimental supportAT rich regionsICESau7215311Meng LIU (Mia), Oliver He250http://202.120.12.136/ICEberg2/feature_page.php?ice_id=250ICE with experimental supportAT rich regionsICESau7312330Meng LIU (Mia), Oliver He253http://202.120.12.136/ICEberg2/feature_page.php?ice_id=253ICE with experimental supportAT rich regionsICESau7412791Meng LIU (Mia), Oliver He248http://202.120.12.136/ICEberg2/feature_page.php?ice_id=248ICE with experimental supportAT rich regionsICESau7413093Meng LIU (Mia), Oliver He257http://202.120.12.136/ICEberg2/feature_page.php?ice_id=257ICE with experimental supportAT rich regionsICESau7413714Meng LIU (Mia), Oliver He249http://202.120.12.136/ICEberg2/feature_page.php?ice_id=249ICE with experimental supportAT rich regionsICESau7512166Meng LIU (Mia), Oliver He258http://202.120.12.136/ICEberg2/feature_page.php?ice_id=258ICE with experimental supportAT rich regionsICESau7512986Meng LIU (Mia), Oliver He267http://202.120.12.136/ICEberg2/feature_page.php?ice_id=267ICE with experimental supportAT rich regionsICESau7611280Meng LIU (Mia), Oliver He259http://202.120.12.136/ICEberg2/feature_page.php?ice_id=259ICE with experimental supportAT rich regionsICESau7612628Meng LIU (Mia), Oliver He256http://202.120.12.136/ICEberg2/feature_page.php?ice_id=256ICE with experimental supportAT rich regionsICESau7711730Meng LIU (Mia), Oliver He245http://202.120.12.136/ICEberg2/feature_page.php?ice_id=245ICE with experimental supportAT rich regionsICESau8797Meng LIU (Mia), Oliver He251http://202.120.12.136/ICEberg2/feature_page.php?ice_id=251ICE with experimental supportAT rich regionsICESau9877324Meng LIU (Mia), Oliver He262http://202.120.12.136/ICEberg2/feature_page.php?ice_id=262ICE with experimental supportAT rich regionsICESauST398Meng LIU (Mia), Oliver He255http://202.120.12.136/ICEberg2/feature_page.php?ice_id=255ICE with experimental supportAT rich regionsICESauSW356Meng LIU (Mia), Oliver He266http://202.120.12.136/ICEberg2/feature_page.php?ice_id=266ICE with experimental supportAT rich regionsICESauUSA42Meng LIU (Mia), Oliver He91http://202.120.12.136/ICEberg2/feature_page.php?ice_id=91Enterococcus faecalis; Listeria monocytogenes;Enterococcus faeciumICE with experimental supportTn1545Meng LIU (Mia), Oliver He330http://202.120.12.136/ICEberg2/feature_page.php?ice_id=330ICE with experimental supportAT rich regionsTn3872Meng LIU (Mia), Oliver He857http://202.120.12.136/ICEberg2/feature_page.php?ice_id=857ICE with experimental supportA+T richTn5031Meng LIU (Mia), Oliver He858http://202.120.12.136/ICEberg2/feature_page.php?ice_id=858ICE with experimental supportA+T richTn5032Meng LIU (Mia), Oliver He859http://202.120.12.136/ICEberg2/feature_page.php?ice_id=859ICE with experimental supportA+T richTn5033Meng LIU (Mia), Oliver He99http://202.120.12.136/ICEberg2/feature_page.php?ice_id=99~19 kbICE with experimental supportTn5381Meng LIU (Mia), Oliver He100http://202.120.12.136/ICEberg2/feature_page.php?ice_id=100~20 kbICE with experimental supportTn5383Meng LIU (Mia), Oliver He104http://202.120.12.136/ICEberg2/feature_page.php?ice_id=104Klebsiella pneumoniae; Serratia liquefaciens; Pseudomonas sp.; Enterococcus sp. and Streptococcus sp.ICE with experimental supportTn6009Meng LIU (Mia), Oliver He860http://202.120.12.136/ICEberg2/feature_page.php?ice_id=860ICE with experimental supportTn6194 [CTnCD11]Meng LIU (Mia), Oliver He105http://202.120.12.136/ICEberg2/feature_page.php?ice_id=105Streptococcus spp.ICE with experimental supportTn916SMeng LIU (Mia), Oliver He106http://202.120.12.136/ICEberg2/feature_page.php?ice_id=106~23 kbStreptococcus faecalis; Steptococcus lactisICE with experimental supportTn919Meng LIU (Mia), Oliver He4http://202.120.12.136/ICEberg2/feature_page.php?ice_id=4~52 kbBacteroides spp.ICE with experimental supportFew sitesCTnERLMeng LIU (Mia), Oliver He3http://202.120.12.136/ICEberg2/feature_page.php?ice_id=3~65 kbBacteroides thetaiotaomicron; Bacteroides spp.; Escherichia coliICE with experimental supportTTTGCNNNNNCTnDOTMeng LIU (Mia), Oliver He57http://202.120.12.136/ICEberg2/feature_page.php?ice_id=57Pseudomonas putida; Pseudomonas aeruginosa; Cupriavidus necatorICE with experimental supporttRNA-GlyICEclc(JS705)Meng LIU (Mia), Oliver He75http://202.120.12.136/ICEberg2/feature_page.php?ice_id=75501.8 kb59.3ICE with experimental supporttRNA-PheICEMlSym(R7A)Meng LIU (Mia), Oliver He95http://202.120.12.136/ICEberg2/feature_page.php?ice_id=95~47.5 kbICE with experimental supportTn5252 (part of Tn5253)Meng LIU (Mia), Oliver He367http://202.120.12.136/ICEberg2/feature_page.php?ice_id=367ICE with experimental supportICESpnJ93183Meng LIU (Mia), Oliver He368http://202.120.12.136/ICEberg2/feature_page.php?ice_id=368ICE with experimental supportICESpnJ93292Meng LIU (Mia), Oliver He365http://202.120.12.136/ICEberg2/feature_page.php?ice_id=365ICE with experimental supportICESpnKD6Meng LIU (Mia), Oliver He366http://202.120.12.136/ICEberg2/feature_page.php?ice_id=366ICE with experimental supportICESpnN24Meng LIU (Mia), Oliver He369http://202.120.12.136/ICEberg2/feature_page.php?ice_id=369ICE with experimental supportICESpn2531Meng LIU (Mia), Oliver He370http://202.120.12.136/ICEberg2/feature_page.php?ice_id=370ICE with experimental supportTn5252(SP1000)Meng LIU (Mia), Oliver He363http://202.120.12.136/ICEberg2/feature_page.php?ice_id=363>67 kbICE with experimental supportICESpnA213Meng LIU (Mia), Oliver He362http://202.120.12.136/ICEberg2/feature_page.php?ice_id=362>75 kbICE with experimental supportTn1311Meng LIU (Mia), Oliver He826http://202.120.12.136/ICEberg2/feature_page.php?ice_id=826~50 kbStreptococcus pyogenes; Streptococcus agalactiae; Streptococcus pneumoniae; Streptococcus dysgalactiae; Streptococcus gordonii; Streptococcus oralisICE with experimental supportICESpy005IQMeng LIU (Mia), Oliver He805http://202.120.12.136/ICEberg2/feature_page.php?ice_id=805~63 kbStreptococcus pyogenes 12RF; Streptococcus agalactiae 1357RF; Streptococcus suis v36RFICE with experimental supportrplLICESde3396-likeMeng LIU (Mia), Oliver He832http://202.120.12.136/ICEberg2/feature_page.php?ice_id=83289 kbICE with experimental supportTTATTTAAGAGTAACICESsuHB1011Meng LIU (Mia), Oliver He73http://202.120.12.136/ICEberg2/feature_page.php?ice_id=7322.3 kbICE with experimental supportpdhA, orf251ICEF-IIMeng LIU (Mia), Oliver He110http://202.120.12.136/ICEberg2/feature_page.php?ice_id=110~90 kbICE with experimental supportbph-salMeng LIU (Mia), Oliver He1http://202.120.12.136/ICEberg2/feature_page.php?ice_id=1~52 kbBacteroides spp.; Escherichia coliICE with experimental supportBTF-37Meng LIU (Mia), Oliver He63http://202.120.12.136/ICEberg2/feature_page.php?ice_id=63Bacteroides fragilisICE with experimental supportCTn86Meng LIU (Mia), Oliver He65http://202.120.12.136/ICEberg2/feature_page.php?ice_id=65~75 kbBacteroides spp.ICE with experimental supportCTnGERM1Meng LIU (Mia), Oliver He1078http://202.120.12.136/ICEberg2/feature_page.php?ice_id=107865 kbLegionella pneumophila JR32 pcsrT(MB1384)ICE with experimental supporttRNAArgICE-&beta;oxMeng LIU (Mia), Oliver He942http://202.120.12.136/ICEberg2/feature_page.php?ice_id=94287.6 kbother rhizobiaICE with experimental supportgly-tRNAICE(Ac)Meng LIU (Mia), Oliver He669http://202.120.12.136/ICEberg2/feature_page.php?ice_id=669Streptococcus agalactiae Nem316; Streptococcus agalactiae COH1; Streptococcus pyogenes (ATCC 12202)ICE with experimental supporttRNALysICE_515_tRNALysMeng LIU (Mia), Oliver He673http://202.120.12.136/ICEberg2/feature_page.php?ice_id=67342.8 kbonly in Streptococcus agalactiaeICE with experimental supporttRNALysICE_FSLS3-026_tRNALysMeng LIU (Mia), Oliver He876http://202.120.12.136/ICEberg2/feature_page.php?ice_id=87647.1 kbICE with experimental supportintergenicICE_SagNEM316_TnGBS1_1Meng LIU (Mia), Oliver He966http://202.120.12.136/ICEberg2/feature_page.php?ice_id=96662.8 kbICE with experimental supportmutYICEEa1Meng LIU (Mia), Oliver He987http://202.120.12.136/ICEberg2/feature_page.php?ice_id=98792.3 kbPasteurella multocida40.18[41.05]ICE with experimental supporttRNALeu (DR:5'-GATTTTGAATC-3')ICEMh1Meng LIU (Mia), Oliver He787http://202.120.12.136/ICEberg2/feature_page.php?ice_id=787Streptococcus pyogenes RF12ICE with experimental supportICESa2603/ICESsu32457Meng LIU (Mia), Oliver He790http://202.120.12.136/ICEberg2/feature_page.php?ice_id=790~110 kbStreptococcus agalactiae 1357RF; Streptococcus pyogenes 12RFICE with experimental support3' end of the rplLICESag236Meng LIU (Mia), Oliver He793http://202.120.12.136/ICEberg2/feature_page.php?ice_id=793~129 kbStreptococcus agalactiae 1357RFICE with experimental supportrplLICESagTR7Meng LIU (Mia), Oliver He814http://202.120.12.136/ICEberg2/feature_page.php?ice_id=814~53.0 kbStreptococcus pyogenes 24RFICE with experimental support3' end of the conserved rumICESp2906Meng LIU (Mia), Oliver He1038http://202.120.12.136/ICEberg2/feature_page.php?ice_id=103814.9 kbThermus thermophilus HB858[68]ICE with experimental support3' end of an isoleucine tRNAICEth1Meng LIU (Mia), Oliver He1080http://202.120.12.136/ICEberg2/feature_page.php?ice_id=1080Legionella pneumophila JR32 pcsrT(MB1384)ICE with experimental supporttRNAMetLpgGI-1Meng LIU (Mia), Oliver He111http://202.120.12.136/ICEberg2/feature_page.php?ice_id=111~65 kb38ICE with experimental supporttRNA-PheLpPI-1Meng LIU (Mia), Oliver He1088http://202.120.12.136/ICEberg2/feature_page.php?ice_id=108898.5 kbICE with experimental supportPbN1_GI15Meng LIU (Mia), Oliver He542http://202.120.12.136/ICEberg2/feature_page.php?ice_id=54214.6 kbSaccharopolyspora spinosaKM26075467.21..14611ICE with experimental supporttRNA(Ser)pCM32Meng LIU (Mia), Oliver He120http://202.120.12.136/ICEberg2/feature_page.php?ice_id=12013.6 kbStreptomyces lividansICE with experimental supportpIJ110Meng LIU (Mia), Oliver He119http://202.120.12.136/ICEberg2/feature_page.php?ice_id=11915 kbStreptomyces lividansICE with experimental supporttRNA-ThrpIJ408Meng LIU (Mia), Oliver He122http://202.120.12.136/ICEberg2/feature_page.php?ice_id=12223.3 kbEU14976568.441..23290ICE with experimental supporttRNA-PhepMEA100Meng LIU (Mia), Oliver He123http://202.120.12.136/ICEberg2/feature_page.php?ice_id=12313.3 kbL3667969.351..13285ICE with experimental supporttRNA-IlepMEA300Meng LIU (Mia), Oliver He150http://202.120.12.136/ICEberg2/feature_page.php?ice_id=15011.2 kbAY86011067.571..11188ICE with experimental supporttRNA-PhepMR2Meng LIU (Mia), Oliver He124http://202.120.12.136/ICEberg2/feature_page.php?ice_id=12448.4ICE with experimental supportpRS01Meng LIU (Mia), Oliver He118http://202.120.12.136/ICEberg2/feature_page.php?ice_id=1189 kbNC_00211268.731..9014ICE with experimental supportpSA1.1Meng LIU (Mia), Oliver He117http://202.120.12.136/ICEberg2/feature_page.php?ice_id=11710.9 kbStreptomyces lividansICE with experimental supporttRNA-PropSAM2Meng LIU (Mia), Oliver He157http://202.120.12.136/ICEberg2/feature_page.php?ice_id=15717.3 kbAM42029368.99[71.15]7823295..7840549ICE with experimental supporttRNA-Phe(SACE_8046)pSE211Meng LIU (Mia), Oliver He151http://202.120.12.136/ICEberg2/feature_page.php?ice_id=151~16.9 kbICE with experimental supporttRNA-SerpSG1Meng LIU (Mia), Oliver He163http://202.120.12.136/ICEberg2/feature_page.php?ice_id=16317.2 kbStreptomyces lividansNC_00388867.94[72.12]5038594..5055797ICE with experimental supporttRNA-TyrSLP1Meng LIU (Mia), Oliver He93http://202.120.12.136/ICEberg2/feature_page.php?ice_id=9370~80 kbICE with experimental supportTcr Emr 7853Meng LIU (Mia), Oliver He94http://202.120.12.136/ICEberg2/feature_page.php?ice_id=94~150 kbICE with experimental supportTn5030Meng LIU (Mia), Oliver He96http://202.120.12.136/ICEberg2/feature_page.php?ice_id=96~70 kbLactococcus lactisICE with experimental supportTn5276Meng LIU (Mia), Oliver He97http://202.120.12.136/ICEberg2/feature_page.php?ice_id=97ICE with experimental supportTn5281Meng LIU (Mia), Oliver He404http://202.120.12.136/ICEberg2/feature_page.php?ice_id=404~70 kbICE with experimental supportTTTTTGTn5301Meng LIU (Mia), Oliver He98http://202.120.12.136/ICEberg2/feature_page.php?ice_id=98~70 kbICE with experimental supportTn5307Meng LIU (Mia), Oliver He382http://202.120.12.136/ICEberg2/feature_page.php?ice_id=382ICE with experimental supportTn5382(5-F9)Meng LIU (Mia), Oliver He101http://202.120.12.136/ICEberg2/feature_page.php?ice_id=101~65 kbICE with experimental supportalkyl hydrogen peroxide reductase genesTn5385Meng LIU (Mia), Oliver He107http://202.120.12.136/ICEberg2/feature_page.php?ice_id=107ICE with experimental supportTnB1230Streptomyces parvulus ATCC 12434Streptomyces griseus NRRL3851the integration and excision module of ICE Tn919.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/Tn919 IEMthe integration and excision module of ICE TnB1230.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/TnB1230 IEMthe integration and excision module of ICE pJY1.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/pJY1 IEMthe integration and excision module of ICE R997.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/R997 IEMthe integration and excision module of ICE bph-sal.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/bph-sal IEMthe integration and excision module of ICE LpPI-1.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/LpPI-1 IEMthe integration and excision module of ICE ICESb1.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/ICESb1 IEMthe integration and excision module of ICE pSAM2.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/pSAM2 IEMthe integration and excision module of ICE pSA1.1.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/pSA1.1 IEMthe integration and excision module of ICE pIJ408.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/pIJ408 IEMthe integration and excision module of ICE pIJ110.Meng LIU (Mia), Oliver Hehttp://db-mml.sjtu.edu.cn/ICEberg/pIJ110 IEM